Characterization of the autoregulation of simian virus 40 gene A

Cells infected by tsA mutants of simian virus 40 (SV40) overproduce early RNA. Overproduction results from failure of the temperature-sensitive A protein (T antigen) to inhibit early transcription. The amount of early RNA in the cytoplasm, determined quantitatively from the kinetics of hybridization to labeled complementary SV40 DNA, was elevated at both permissive (32 degrees C) and nonpermissive (41 degrees C) temperatures in all the early mutants tested (tsA7, -30, -58, and -209), but not in the late mutant tsB4. The amount of early RNA in a culture maintained at 32 degrees C for 72 h and then shifted to 41 degrees C was maximum when each cell was infected initially with at least one plaque-forming unit of tsA58. Azidocytidine (2'-deoxy-2'-azidocytidine), which inhibits initiation of DNA synthesis, did not cause overproduction of early RNA in cells infected with wild-type SV40, showing that the effect seen with tsA mutants is not due to interference with initiation of DNA synthesis per se. In parallel infections at 41 degrees C, the amount of early RNA per copy of viral DNA was as much as 2,000 times greater with tsA58 than with wild-type SV40, even though there was no replication of the tsA58 DNA. Synthesis of late RNA could not be detected during the first 20 h of an infection by either virus at 32 degrees C, indicating that late and early transcription are under different control. In three cell lines transformed by tsA mutants, the amount of early RNA increased moderately after a shift from 32 to 41 degrees C, whereas with homologous cells transformed by wild-type virus, the amount of early RNA decreased, indicating that the A protein may be able to repress transcription of integrated SV40 DNA. All the observations are consistent with a simple model in which the binding of A protein at the origin of replication blocks either binding of RNA polymerase to the early promoter or its progress through the early gene(s).

Transcription of the argF and argI genes of the arginine biosynthetic regulon of Escherichia coli K12, performed in vitro

The cell-free transcription of the argF and argI genes of the arginine biosynthetic regions is described using an S-30 system capable of coupled in vitro transcription-translation. Template DNA isolated from two independently isolated arginine transducing phages was used in this work. Steady state mRNA synthesis was observed which was attributed to RNAase degradation. Regulation of argF mRNA synthesis, directed by the argF gene carried on the specialized transducing phage phi80dargF is effected to the extent of at least 95% by the arginine holorepressor at the transcriptional stage and at least 80% of the regulation of the expression of the argI gene is mediated at the transcriptional stage. Evidence is presented which indicates that the arginine holorepressor prevents RNA polymerase from binding to the arginine promoter and suggests that the operator and promoter sites may overlap.

Synthesis and biological activity of a lambda pseudo operator

The chemical and enzymatic syntheses of bacteriophage lambda pseudo operator DNA are described. The 17 base-paired duplex contains the DNA which has been proposed as the binding site for cI repressor protein. The synthetic duplex is twofold symmetric and represents the best possible nucleotide summation of the six proposed operator sites in the leftward and rightward operators. However, it does not correspond exactly to any single proposed operator sequence. The chemical synthesis includes the deoxyoligonucleotides d(T-A-T-C-A-C), d(C-G-C-C-G-G-T-G-A-T-A), d(T-A-T-C-A-C-C), and d(G-G-C-G-G-T-G-A-T-A). These deoxyoligonucleotides were joined with T4 DNA ligase to form d(T-A-T-C-A-C-C-G-C-C-G-G-T-G-A-T-A) and d(T-A-T-C-A-C-C-G-G-C-G-G-T-G-A-T-A). The cI repressor protein was found to bind to the duplex formed from these two segments.

RNA-linked nascent DNA pieces in T7 phage-infected Escherichia coli cells. I. Role of gene 6 exonuclease in removal of the linked RNA

The presence of RNA-linked nascent DNA pieces in T7 phage-infected Escherichia coli cells has been shown by the selective degradation of the 5'-hydroxyl-terminated nascent DNA, produced by alkali or RNase treatment, with spleen exonuclease. At 43 degrees C, the proportion of RNA-linked DNA pieces in nascent short dna is 50 to 60% in T7 ts136 (ts mutant of gene 6) phage-infected E. coli, whereas that in T7 wild-type phage-infected cells is less than 6%. Joining of the nascent pieces is greatly retarded in T7 ts136-infected E. coli temperature sensitive polA mutants at 43 degrees C. These results suggest that gene 6 exonuclease plays a role in removal of the linked RNA during the discontinuous replication of T7 DNA.

Genetic identification of cloned fragments of bacteriophage T4 DNA and complementation by some clones containing early T4 genes

Bacteriophage T4 DNA containing cytosine has been obtained from cells infected with phage mutant in genes 42, 56, denA and denB. This DNA can be cut by a number of restriction endonucleases. Fragments obtained by digestion of this DNA with EcoRI have been cloned using the vector plasmid pCR1. Clones containing T4 DNA were identified by hybridization with radioactive early and late T4 RNA. A simple marker rescue technique is described for the genetic identification of the cloned T4 fragments. Some of the T4-hybrid plasmids which contain entire T4 genes can complement temperature sensitive and amber mutants of T4.

HindII, HindIII, and HpaI restriction fragment maps of bacteriophage lambda DNA

The site-specific restriction endonucleases isolated from Hemophilus influenzae strains Rc (HincII) and Rd (HindII + III), and Hemophilus parainfluenzae (HpaI) were used to digest bacteriophage lambda DNA into 34, 40, and 15 specific fragments, respectively. The sites cleaved by each of these enzymes were localized on the lambda physical map and the fragments resulting from these cleavages were electrophoretically identified on gels by (1) analysis of the digestion profiles of deletion and transducing derivatives of lambda; and (2) digesting individual fragments produced by one restriction endonuclease with another restriction endonuclease. This paper presents the HindII, HindIII, and HpaI restriction fragment maps for the entire lambda genome, and the data used to derive these maps for the region of the lambda genome between the attachment site (at 57.3% lambda) and the right vegetative end (100% lambda). The data for mapping the left arm of lambda may be found in the accompanying paper (Robinson and Landy, 1977).

Cell fusion induced by herpes simplex virus is promoted and suppressed by different viral glycoproteins

Some of the factors that regulate membrane fusion resulting in polykaryocyte formationhave been investigated, using the model system of human cells infected with mutants of herpes simplex virus (HSV). One of the mutant viruses used in this study (MP) failed to produce the viral glycoprotein designated C2--a nonlethal defect that has previously been correlated with the polykaryocyte-inducing phenotype of this and other mutant strains (wild-type strains of HSV usually induce the aggregation of infected cells rather than their fusion). The other mutant virus (tsB5), a temperature-sensitive conditional-lethal mutant, failed to produce glycoprotein B2 at non-permissive temperature, whereas the synthesis of all other viral products appeared to be normal. We produced and isolated seven recombinants of MP and tsB5 that expressed both of the parental alterations in glycoprotein synthesis. All of the re-combinant viruses induced the fusion of infected cells at 34 degrees (correlated with the absence of C2 expression) but were unable to cause cell fusion at 39 degrees (correlated with the absence of C2 and of B2 expression), even after infection at multiplicities high enough to ensure that all cells in the cultures synthesized viral macromolecules. These results and studies on the dominance or recessiveness of the fusion-inducing phenotype in mixed infections provide evidence that glycoprotein B2 plays a critical role in the promotion of cell fusion and that glycoprotein C2 can act to suppress fusion.

Filamentous coliphage M13 as a cloning vehicle: insertion of a HindII fragment of the lac regulatory region in M13 replicative form in vitro

A HindII restriction fragment comprising the Escherichia coli lac regulatory region and the genetic information for the alpha peptide of beta-galactosidase (beta-D-galactosidegalactohydrolase, EC. 3.2.1.23) has been inserted into 1 of the 10 Bsu I cleavage sites of M13 by blunt end ligation. A stable hybrid phage was isolated and identified by its ability to complement the lac alpha function. Further characterization of the hybrid phage includes retransformation studies, agarose gel electrophoresis, DNA-DNA hybridization, and heteroduplex mapping. The insertion point has been localized at 0.083 map unit on thewild-type circular map-i.e., within the intergenic region. The results prove that part of the intergenic region is nonessential and that the phage can be used as a cloning vehicle.

Further mapping of late adenovirus genes by cell-free translation of RNA selected by hybridization to specific DNA fragments

RNA isolated from the cytoplasm of human cells at late times after infection by adenovirus type 2 (Ad2) has been fractionated by hybridization to fragments of Ad2 DNA which were produced by digestion with the restriction endonucleases Hpa I, Eco RI, Bam HI and Hind III. Cell-free translation of these partially purified mRNAs indicates that the genes for the late Ad2 proteins lie within the following intervals on the conventional Ad2 map: 15K (4.4-17.0 map units), IX and IVa2 (7.5-17.0), IIIa (29.1-40.9), III and V (29.1-57.0), pVIII (40.9-57.0), pVI and II (40.9-70.7), 100K (59.0-83.4), pVIII (70.7-83.4) and IV (85.0-100). In addition to the primary hybridization of the late Ad2 mRNAs to the regions indicated above, most late Ad2 mRNAs (except those for 15K, IX and IVa2) exhibited some hybridization to a secondary site between 17.0 and 29.1 map units.

Novel mechanism for RNA maturation: the leader sequences of simian virus 40 mRNA are not transcribed adjacent to the coding sequences

The 5'-terminal 100-200 ribonucleotides of late simian virus 40 (SV40) mRNAs are not transcribed immediately adjacent to their coding sequences. This conclusion is based on the following observations. The major late SV40 cytoplasmic RNA species, 16S and 19S, were purified from poly(A)-containing cytoplasmic RNA by hybridization to and elution from an SV40 DNA fragment that maps between 0.67 and 0.76. This fragment is remote from the DNA fragments that include the coding sequences. The RNA transcripts from the fragment located between 0.67 and 0.76 were found in abundance. Even though selected on oligo(dT)-cellulose columns, the 5'-terminal sequences did not contain poly(A) tails directly adjacent to their 3' termini. The 5' terminus of the 16S mRNA, as monitored by hybridization of the sequences adjacent to the "cap" structure, was found adjacent to the coding sequences when intact [3H]methyl-labeled RNA was hybridized with restriction fragments. However, after fragmentation, the methyl label of this same RNA hybridized with a fragment that is remote from the coding sequences and maps between 0.67 and 0.73. These results imply a novel mechanism for biosynthesis of SV40 mRNA.

Two adenovirus mRNAs have a common 5' terminal leader sequence encoded at least 10 kb upstream from their main coding regions

The messenger RNAs encoding two late adenovirus serotype 2 (Ad2) proteins, fiber and 100K, were purified by hybridization to restriction endonuclease fragments of Ad2 DNA followed by electrophoresis on polyacrylamide gels containing 98% formamide. The 5' terminal oligonucleotides generated by RNAase T1 digestion of the messengers were selected by dihydroxyboryl-cellulose chromatography. Both mRNAs gave an identical 5'-undecanucleotide with the general structure 7mG5'ppp5'AmC(m)U(C4,U3)G. This undecanucleotide could be removed by mild RNAase treatment from the mRNA after hybridization to DNA fragments containing the main coding sequence of the messenger. In contrast, a small region defined by Bal I-E (14.7-21) protects this undecanucleotide from RNase. A second region contained within both Hind III-B (17-31.5) and Hpa I-F (25.5-27.9), although unable to protect the undecanucleotide, hybridizes to both fiber and 100K mRNAs and protects a similar sequence of 100-150 nucleotides. These observations suggest that both mRNAs contain a long common sequence, complementary to at least two different sites on the Ad2 genome remote from the start of these two genes. The implications of these findings are discussed, and a general mechanism is presented for the biosynthesis of mRNAs from larger precursor molecules, based on intramolecular ligation.

Peptide mapping of 125I-labelled influenza virus proteins. Matrix proteins as markers in recombination

We have examined the matrix proteins of A/Okuda/57, A/Finland/4/74 and A/New Jersey/8/76 viruses and several recombinant strains by radioiodination of the purified polypeptides followed by tryptic peptide mapping. The method is rapid and requires only small amounts of material. Reproducible differences were detected between the matrix proteins of the above parents and allowed origin of the matrix proteins of the recombinant viruses to be determined. The possible use of matrix protein identity as a marker in recombination work is discussed.

Internal proteins of influenza virus: 35S-methionine peptide maps as genetic markers

Methods are described for the preparation in vivo of 35S-methionine-labelled influenza viruses, the purifiction of the nucleoprotein (NP) and matrix (M) proteins and the separation of peptides obtained by protease digestion by two-dimensional thin-layer chromatography. The maps of the M proteins of A/Okuda/57(H2N2) and A/Finland/4/74(H3N2) were very similar overall but differed in three peptides. Hence they could be clearly distinguished. Maps of the NP proteins of the same strains showed a greater number of differences. A recombinant strain having the haemagglutinin and neuraminidase of the A/Finland/4/74 parent and the virulence of the A/Okuda/57 parent was shown to have the M and P proteins of A/okuda/57.

A novel method to map transcripts: evidence for homology between an adenovirus mRNA and discrete multiple regions of the viral genome

A method has been devised which permits mapping of transcripts by a two-step hybridization procedure (sandwich hybridization). RNA extracted from cells infected with an adenovirus-SV40 hybrid (Ad2+ND1) was hybridized to restriction endonuclease fragments of adenovirus type 2 (Ad2) DNA immobilized on nitrocellulose filters. RNAs containing both Ad2 and SV40 sequences formed duplexes through their Ad2 sequences, leaving their SV40 sequences as protruding tails. Annealing with 32P-labeled SV40 DNA caused these tails to become labeled, permitting autoradiographic identification of the sequences of Ad2 DNA which are homologous to the RNA. The high sensitivity of this technique, achieved through the use of 32P-labeled RNA of high specific activity, has led to the observation that hybridization of Ad2+ND1 RNA occurs at several locations on the Ad2 genome, in addition to the expected sites of hybridization proximal to the SV40 insertion.

An amazing sequence arrangement at the 5' ends of adenovirus 2 messenger RNA

The 5' terminal sequences of several adenovirus 2 (Ad2) mRNAs, isolated late in infection, are complementary to sequences within the Ad2 genome which are remote from the DNA from which the main coding sequence of each mRNA is transcribed. This has been observed by forming RNA displacement loops (R loops) between Ad2 DNA and unfractionated polysomal RNA from infected cells. The 5' terminal sequences of mRNAs in R loops, variously located between positions 36 and 92, form complex secondary hybrids with single-stranded DNA from restriction endonuclease fragments containing sequences to the left of position 36 on the Ad2 genome. The structures visualized in the electron microscope show that short sequences coded at map positions 16.6, 19.6 and 26.6 on the R strand are joined to form a leader sequence of 150-200 nucleotides at the 5' end of many late mRNAs. A late mRNA which maps to the left of position 16.6 shows a different pattern of second site hybridization. It contains sequences from 4.9-6.0 linked directly to those from 9.6-10.9. These findings imply a new mechanism for the biosynthesis of Ad2 mRNA in mammalian cells.

[Factors involved in the development of human tumors using the Epstein-Barr virus as an example (author's transl)]

Several viruses induce tumors in animals under experimental or natural conditions. It is likely therefore that some human malignancies are also caused by viruses. Proof of this hypothesis can be provided only by indirect evidence based on the following criteria: (1) detection of viral antigens or viral genetic information in a given tumor; (2) transformation of normal human cells by the virus in tissue culture; (3) induction of tumors in animals by the virus; and (4) demonstration of enhanced titers of antibodies to the virus in patients bearing the tumor. These criteria have been fulfilled to support a causal relationship of the Epstein-Barr virus (EBV) in Burkitt's lymphoma and nasopharyngeal carcinoma. It is clear, however, that factors of a genetic, immunologic or environmental nature must play an additional role because EBV, the cause of infectious mononucleosis, is widely disseminated yet development of the tumors is a rare event.

Genetic information analysis of bacteriophage phiX 174

The genetic information of phix 174 genome (genes and intermediate segments) is analyzed in terms of its independent (D1 index) and dependent information (D2 and D3 Markovian indexes), as well as of its ability to generate secondary structure. Genes B and E, enclosed in A and D respectively, have: 1) values of D1 and D3 indexes closer to the theoretical random distribution curves than those of (A-B) and (D-E) gene fractions, and 2) in the ability for secondary structure generation minor differences with genes A and D. F leads to G and mRNA start leads to A intermediate segments differ from randomness in their D1 and D2 indexes, but not so much in the D3 values. All these data point out the use of code degeneracy for increasing the genetic information density of the virus.

Viral DNA sequences from incomplete particles of human adenovirus type 7

Large pools of empty viral capsids accumulate in cells infected by subgroup B human adenoviruses. Such infected cells also yield DNA-containing incomplete particles in larger quantities than cells infected with serotypes representing other adenovirus subgroups. DNA isolated from carefully purified classes of Ad7 incomplete particles was analyzed by restriction endonuclease cleavage, gel electrophoresis and electron microscopy. At least 90% of the DNA molecules in each sample consisted of sequences that extended from the left end of the viral genome map by variable lengths toward the right end. The average length of DNA is linearly related to the average buoyant density of the incomplete particles from which the DNA is isolated. The results indicate that each capsid contains one DNA molecule. There is also a specific association of the left end of the viral genome with assembled or assembling capsids. The characteristic distributions of Ad7 incomplete particles may result from intracellular pools of assembly intermediates in which the incompletely packaged DNA has been fragmented in vivo or by shear during preparative procedures.

[Model studies on virus-induced tumors and their immunological treatment (author's transl)]

After a review of the general biological properties of C-type oncorna viruses, results are presented on the structure of an exogenous murine leukemia virus (FLV) and on the serobiological properties of its structural proteins. Our findings suggested a major role of the viral surface glycoprotein gp71 in immunological defense mechanisms. This was confirmed by vaccination experiments with isolated gp71 in mice. The induced immunity was highly specific and not operative against endogenous murine C-viruses belonging to other serotypes. Surprisingly the latter were found to be activated by the vaccination with gp71 of FLV. In heterologous animal species isolated FLV-gp71 induced the formation of broadly reacting antibodies. They were found to be effective in the therapy of infections with FLV in mice as well as with feline leukaemia virus in cats. Most impressive results were obtained with an antiserum prepared against feline leukaemia virus in a goat. This serum completely suppressed sarcomas induced by infection with feline sarcoma virus.

The significance and nature of defective interfering viruses

Deletions in viral genomes appear to be a common occurrence in the replication of all DNA and RNA viruses which have been adequately studied. Such defective genomes can replicate in the presence in the same cell of a helper virus as long as the deletion does not involve the initiation site for genome replication. Coinfection of a cell with defective and "normal" infectious virus leads to reduction in the yield of the latter. The nature of DI viruses and genomes found in Sindbis virus-infected vertebrate cells during "undiluted passage" series is discussed. This procedure leads to the accumulation of progressively shorter viral RNA genomes with internal deletions. The enrichment is limited to genome lengths which are integral fractions (1/2, 1/3, 1/4, etc.) of the complete genome, and these are also found in viral particles released at the corresponding passage levels. It is believed that the selective accumulation of these fragments is governed by constraints of assembly which demand that one full genome equivalent be packaged in a released particle. In contrast to vertebrate cells, cultured mosquito cells do not seem to produce or "recognize" DI particles. Possible implications for the epidemiology of arthropod-transmitted alphaviruses are presented.

Involvement of DNA-dependent RNA polymerase in a recA-independent pathway of genetic recombination in Escheria coli

Recombinant DNA molecule of phage lambda formed in Escherichia coli in the presence of chloramphenicol and/or rifampin can be assayed by their biological activity. recA- cells were found to be capable of forming recombinant lambda phage DNA in the presence of chloramphenicol. The relatively high recA-independent recombination observed in this system contrasts with the relatively low recA-independent recombination when recombinant phage particles rather than recombinant DNA are titrated. Formation of the recombinant DNA was suppressed by the the addition of rifampin. The introduction of the rif-r mutation into host bacteria made their recombination activity rifampin-resistant. These results show that DNA-dependent RNA polymerase (EC 2.7.7.6) is involved in this recA-independent pathway of recombination, which is named the "Rpo pathway." This is distinct from Red, Int, RecBC, RecE, or Der pathways of recombination. Crossover was much more frequent in the N-PL-cI and cI-PR-O regions than in the A-D and O-S regions. The crossover seems to occur in the regions that are transcribed actively. Some local change of DNA structure caused by transcription might be required for the Rpo pathway of recombination.

HindII, HindIII, and HpaI restriction fragment maps of the left arm of bacteriophage lambda DNA

The sites on the left arm of bacteriophage lambda DNA cleaved by the restriction endonucleases isolated from Hemophilus influenzae strain Rc (HincII) and Rd (HindII + III), and Hemophilus parainfluenzae (HpaI) were localized on the lambda physical map, and the fragments resulting from these cleavages were identified by gel electrophoresis. The restriction sites within the b2 region of lambda were mapped by analysis of the digestion profiles of deletion and substitution derivatives of lambda, as well as by digesting individual fragments produced by one restriction endonuclease with another restriction endonuclease. The restriction sites of the lambda genome between the left vegetative end and the b2 region were mapped entirely by succesive digestion experiments. The restriction fragment map for the right arm of lambda may be found in the accompanying paper (Robinson and Landy, 1977).

Electron microscopy analysis of the interaction between Escherichia coli DNA-dependent RNA polymerase and the replicative form of phage fd DNA. 1. Mapping of the binding sites

The interaction of Escherichia coli DNA-dependent RNA polymerase (EC 2.7.7.6) with the replicative form of the DNA from the filamentous coliphage fd cleaved by the restriction endonuclease HindII has been studied by electron microscopy at low and high ionic strength. In the presence of ATP or GTP, and heparin, RNA polymerase binds to fd replicative-form DNA at a few specific sites which have been mapped. The map was oriented so that transcription is from right to left. Three main GTP initiator sites are found at 15%, 82% and 94% of the genome length. One main ATP initiator site is found which cannot be mapped with the same accuracy, and which is localized between 38% and 50%. In the absence of initiator triphosphates and heparin, the binding of the enzyme to fd DNA is much more heterogeneous and therefore the mapping is more difficult. Nevertheless it seems that the preferential binding regions correspond to the specific sites mapped in the presence of GTP or ATP. The mean number of polymerase molecules bound to DNA as a function of the molecular ratio enzyme to DNA present in the mixture has been determined. From these results a binding isotherm can be obtained. The apparent equilibrium constant (K approximately 10(9) M-1) which is derived certainly represents an under-estimated value, as discussed.

Bacteriophage T4 RNA ligase is gene 63 product, the protein that promotes tail fiber attachment to the baseplate

RNA ligase and tail fiber attachment activities, normally induced following bacteriophage T4 infection of Escherichia coli, are not induced when gene 63 amber mutants of T4 infect nonpermissive host cells. Both activities are induced when these mutants infect permissive hosts, or when revertants of these mutants infect nonpermissive hosts. When one of these mutants infects a host that carries supF, both activities are more than normally heat labile. RNA ligase, purified to homogeneity, promotes the tail fiber attachment reaction in vitro with a specific activity similar to that of the most highly purified preparations of gene 63 product isolated on the basis of tail fiber attachment activity. We conclude that T4 RNA ligase is gene 63 product. The RNA ligase and tail fiber attachment reactions differ in requirements and in response to some inhibitors, suggesting that the two activities of the gene 63 product may be mechanistically unrelated.

In vitro translation yields a possible Rous sarcoma virus src gene product

In vitro translation of Rous sarcoma virus (RSV) virion RNA in the messenger-dependent reticulocyte lysate system yielded polypeptides that were not synthesized by translation of RNA from a transformation-defective deletion mutant of RSV. These RSV-specific products migrated on sodium dodecyl sulfate/polyacrylamide gels as two doublets of approximately 25,000 and 17,000 daltons. Synthesis of these proteins was not sensitive to inhibition by m7GTP; however, synthesis of the 76,000-dalton precursor of the internal structural proteins was sensitive to inhibition by m7GTP. Tryptic peptide maps showed the 25,000- and 17,000-dalton proteins to be related to one another but to be distinct from the 76,000-dalton protein. The 25,000-dalton protein was translated only from a polyadenylylated RNA of approximately 2500 nucleotides, whereas the 76,000-dalton protein was translated from 38S RNA, corresponding to the entire viral genome. A 180,000-dalton protein was also synthesized from 38S RSV virion RNA. From the absence of the 25,000- and 17,000-dalton proteins in the translation products of transformation-defective RSV RNA and the size of their RNA templates, we conclude that these proteins may be derived from coding sequences within the RSV src gene.

Nucleotide sequence of the gene for the major structural protein of SV40 virus

We have determined the sequence of the portion of Simian Virus 40 (SV40) that codes for the major structural protein of the virus. The gene contains 361 codons. Synonym codons for an amino acid are not used randomly. The dinucleotide CG occurs only once and there is 2 to 1 preference for uridylic acid in the third position of codons.

phiX174 cistron A protein is a multifunctional enzyme in DNA replication

The cistron A protein induced by phage varphiX174 nicks (produces a single-strand break in) the viral strand of the superhelical varphiX duplex DNA, thereby forming a complex with the DNA. The protein, seen bound to the DNA in the electron microscope, was located in the restriction endonuclease fragment between nucleotides 4290 and 4330 on the varphiX map [Sanger, F., Air, G. M., Barrel, B. G., Brown, N. L., Coulson, A. R., Fiddes, J. C., Hutchison, C. A., III, Slocomb, P. M. Y. & Smith, M. (1977) Nature 265, 687-695]. Replication also was initiated at this point, thus identifying the site of cistron A protein nicking and binding as the origin of replication. The cisA-DNA complex (separated from free cistron A protein), upon the addition of Escherichia coli rep protein, ATP, and DNA binding protein, is unwound to generate a single-stranded linear [presumably the nicked (+) strand] and a circular [presumably the (-) strand] molecule. The cisA-DNA complex, upon the further addition of DNA polymerase III holoenzyme and deoxynucleoside triphosphates, supports replication to generate viral, single-stranded circles, as many as 15 circles per cisA-DNA complex. The replicating intermediates seen in the electron microscope are a novel form of "rolling circle" [Gilbert, W. & Dressler, D. H. (1969) Cold Spring Harbor Symp. Quant. Biol. 33, 473-485]. The 5' end (presumably with the cistron A protein bound to it) is locked in the replication fork and loops back to accompany the strand-separation and replication fork around the template [(-) strand] circle. Thus, the multiple functions of cistron A protein include: (i) nicking the viral strand at the origin of replication to initiate a round of replication, (ii) participating in a complex which supports fork movement in strand separation and replication, (iii) nicking again at the regenerated origin to produce a unit-length DNA, and (iv) ligating the newly generated 3'-OH end to the 5'-phosphate-complexed end to form a circular viral molecule.

DNA sequence at the end of the cI gene in bacteriophage lambda

The nucleotide sequence of 57 base pairs near the end of the cI gene in phage lambda is presented. This sequence was determined by direct sequencing techniques and includes the codons for 11 carboxyterminal aminoacids of the cI product, the lambda repressor. The sequence reveals that the cI gene, which has recently been shown to have a unique initiation region, is terminated by a UGA codon. A GUG triplet, which could act as a translation start signal for the rex gene occurs 8 base pairs beyond the cI termination codon. This GUG triplet is preceded by a sequence that could serve as a strong ribosome binding site for the rex message.

DNA regions essential for the function of a bacteriophage fd promoter

The promoter for the major coat protein gene of bacteriophage fd contains a unique sequence. TATAAT, in the non-transcribed region corresponding to the Pribnow box. A R-Hha I cleavage site which destroys functions is located five pairs upstream from the TATAAT sequence (fifteen base pairs upstream from the RNA initiation site). The promoter was cleaved into two fragments by R-Hha I and each promoter fragment was joined to DNA fragments derived from other regions. Ligation of the TATAAT-containing fragment to any of the DNA fragments examined resulted in recovery of promoter function. The results suggest for this type of promoter that no unique sequence is necessary upstream from the R-Hha I cleavage site although a contiguous DNA chain must be present in this area.

The nucleotide sequence of two restriction fragments located in the gene AB region of bacteriophage S13

The nucleotide sequence of a double stranded DNA fragment from the gene AB region of bacteriophage S13 DNA has been determined. The fragment was isolated as two adjacent shorter fragments by cleavage of S13 replicative form (RF) DNA with restriction endonuclease III from Hemophilus aegyptius. The strands of the fragments were separated electrophoretically and hydrolyzed with T4 endonuclease IV to yield short oligonucleotides which were then sequenced by partial exonuclease digestion. The complete nucleotide sequence of the restriction fragments was obtained by ordering the inter- and intrastrand overlapping oligonucleotide sequences. The adjacent fragments were 190 nucleotides in length. The sequences included a HindII site, an AluI site and two sequences which may be possible transcription initiation sequences, one with an adjacent sequence homologous to the canonical promoter site sequence T-A-T-Pu-A-T-Pu. Examination of the three possible reading frames for translation of the sequence revealed only one possible complete translation product. The postulated partial sequence of gene A protein has a highly positively charged arginine-rich area which may have importance in DNA binding.

Polyacrylamide gel electrophoresis of the RNAs of new influenza virus strains: an epidemiological tool

Recently, we have shown by separating the RNAs and proteins of different influenza A viruses on polyacrylamide gels, that influenza A viruses contain 8 genes corresponding to 8 virus specific proteins. By analyzing the RNA patterns and the protein patterns of different recombinant viruses we, subsequently, succeeded in establishing a complete genetic map for influenza A viruses. These techniques were extended to characterize the genome of new influenza virus isolates. Thus it was found that the human isolate A/Wi/263/76 and the two swine virus isolates, A/swine/Wi/49/76 and A/swine/Wi/50/76 possess identical RNA patterns, which differ from the RNA patterns of other recent swine virus isolates. The human (Wi/263) and the two animal isolates (Wi/49 and Wi/50) were obtained on the same farm suggesting that the animal virus was transmitted from swine to man. This proves that swine viruses may occasionally infect humans without causing a pandemic. A comparative analysis of the different RNA patterns of other swine influenza viruses isolated around the same time at different locations and of those of recent human isolates showed that our polyacrylamide gel technique is a valuable epidemiological tool to identify and and characterize different influenza virus isolates.

Procedures for characterisation of the genetic material of candidate vaccine strains

Two procedures for characterising the genomes of recombinant influenza viruses are described. The first of these involves ribonuclease T4 oligonucleotide fingerpart analysis of separated viral RNAs labelled either in vivo or in vitro and the second utilises polyacrylamide gel electrophoresis to identify the double-stranded molecules formed by hybridisation between the complementary and virion RNAs of two viruses. Although the latter method is more suitable for routine screening purposes, both procedures are suitable for distinguishing between equivalent RNA components of closely related viruses.

Biological, genetic and biochemical characterization of a cold-adapted recombinant A/Victoria/3/75 virus and its evaluation in volunteers

A recombinant virus AA-CR19 was produced that contains RNA segments coding for one polymerase protein, the nucleoprotein and the matrix protein of cold-adapted A/Ann Arbor/6/60, but HA, NA and two other genes coding for polymerase proteins from A/Victoria/3/75. The nonstructural protein gene is probably derived from A/Ann Arbor/6/60, but may contain a spontaneous mutation. Biological characterization of AA-CR19 showed that it possesses the gene(s) responsible for cold-adaptation and temperature-sensitivity of the A/Ann Arbor/6/60 parent. At a dose of 10(7.2) TCID/50. AA-CR19 was found to be immunogenic and attenuated for seronegative volunteers.

Identification of Rauscher murine leukemia virus-specific mRNAs for the synthesis of gag- and env-gene products

Polyadenylylated mRNA isolated from cells infected with Rauscher murine leukemia virus was fractionated by centrifugation in in a denaturing sucrose gradient into different sizes. Each RNA fraction was injected into oocytes of Xenopus laevis and the virus-specific products were analyzed by immunoprecipitation with polyvalent and monospecific antisera against polypeptides of Rauscher murine leukemia virus, and then by gel electrophoresis and scintillation autoradiography. It was shown that a 35S mRNA species directs the synthesis of a precursor of the internal or group-specific antigens of the virion (the gag-gene products). A 22S mRNA species directs the synthesis of two viral envelope polypeptides and their precursor polypeptide (env-gene products). The results indicate that the gag- and env-related polypeptides of Rauscher murine leukemia virus are synthesized uncoordinately and provide evidence for open and closed cistrons on the virus-specific mRNAs.