Co-amplification of multiple regions of the HIV-1 genome by the polymerase chain reaction: potential use in multiple diagnosis.

We have used the polymerase chain reaction (PCR) to detect by co-amplification, multiple regions of the HIV-1 genome in infected cells. Genomic RNA and DNA from productively infected H9 cells were independently extracted and amplified in reactions with and without reverse transcriptase respectively using primer pairs to the gag, env, tat and nef regions of the viral genome in the same reaction mixture. PCR-products were analysed by liquid hybridization with end labelled oligonucleotide probes followed by gel-electrophoresis (oligomer hybridization). The primer pairs were capable of detecting as few as 10 copies of RNA and 10-20 copies of integrated proviral DNA. The ability to co-amplify multiple target regions in the same incubation mixture provides a method for detecting and confirming the presence of HIV-1 in samples for which limited nucleic acid is available. In addition, in reconstitution experiments, the same method was used to detect HIV-1 and HTLV-I simultaneously with comparable sensitivity (20-40 gene copies each). This offers the possibility of simultaneous diagnosis of multiple viral infections, such as those that occur in AIDS, on the same sample preparation.

Kinetics of early HIV-1 gene expression in infected H9 cells assessed by PCR.

The time course of viral gene expression in H9 cells acutely infected with HIV-1 was analysed by the polymerase chain reaction (PCR). Virus-specific sequences were first detected in genomic DNA of H9 cells 1-2 h after infection. RNA for the regulatory genes such as the tat and nef appeared 2-3 h post-infection and RNA for the gag and env at 3 h. The results demonstrate that viral DNA synthesis occurs rapidly after infection of target cells followed by synthesis of viral RNA. Cell-associated reverse transcriptase activity increased after 24 h, while culture supernatant enzyme activity increased later, between 1-5 days. The delay in virus release after rapid integration and transcriptional activity suggests the involvement of additional factors, perhaps both cellular and viral, that control the formation and budding of mature virions.

Assessment by gene amplification and serological markers of transmission of HIV-1 from hemophiliacs to their sexual partners and secondarily to their children.

The transmission of HIV-1 infection from men with hemophilia A to their female sex partners and secondarily to their children was studied by serological markers including antibody, antigen, and HIV genome as detected by the polymerase chain reaction (PCR). Among 27 sex partners of 26 seropositive hemophiliacs, 5 were seropositive-PCR positive (active), 11 were seronegative-PCR positive (latent), and 11 were negative for both. These results were confirmed by testing serial serum samples and paired samples of DNA from peripheral blood mononuclear cells (PBMCs) and serum from seronegative women. PCR negativity in exposed women was correlated with the use of condoms (p less than 0.01). Eight children from five couples were seronegative. However, HIV-1 infection as detected by PCR was transmitted to 60% of exposed children, including one from a seronegative-PCR positive mother.

Complementation of mutants in the Escherichia coli proton-translocating ATPase by cloned DNA from Bacillus megaterium.

Cloned DNA from Bacillus megaterium can complement mutants in the Escherichia coli proton-translocating ATPase. DNA from the E. coli unc operon, which codes for the ATPase, was used in hybridization experiments to probe for homologous DNA in the Gram-positive sporulating bacterium Bacillus megaterium. Such DNA was identified and subsequently cloned into pBR322. In an E. coli in vitro transcription-translation system, the resultant plasmid directed the synthesis of a 52,000 Mr polypeptide which could be precipitated with antiserum to the E. coli F1-ATPase. This plasmid was also capable of complementing E. coli uncA and uncD mutants, defective in the alpha and beta subunits of the ATPase, respectively. Therefore, the cloned B. megaterium DNA carries the genes for the alpha and beta subunits, and perhaps for other subunits, of the proton-translocating ATPase of B. megaterium. These bacillus subunits can be synthesized and assembled in vivo into a functional hybrid E. coli-B. megaterium ATPase.

Sequence of the genes for the beta and epsilon subunits of the ATP synthase of Bacillus megaterium QM B1551.

Four of the genes for the subunits of the proton-translocating ATPase of Bacillus megaterium have been cloned into pBR322. Previous studies have shown that two of these genes, for the alpha and beta subunits, can complement Escherichia coli mutants defective in the genes for those subunits (Hawthorne, C.A., and Brusilow, W.S.A. 1985. J. Biol. Chem. 261, 5245-5248). We report here a restriction map of the cloned region and the complete nucleotide sequence of the genes for the beta and epsilon subunits as well as the deduced amino acid sequences and molecular weights of those subunits.

Characterization of semi-uncoupled hybrid Escherichia coli-Bacillus megaterium F1F0 proton-translocating ATPases.

Cloned atp genes for the proton-translocating ATPase of the obligate aerobe Bacillus megaterium have been demonstrated to be capable of complementing Escherichia coli ATPase (unc) mutants (Hawthorne, C. A., and Brusilow, W. S. A. (1986) J. Biol. Chem. 261, 5245-5248). To determine the minimum subunit requirements for cross-species complementation, we constructed all combinations of B. megaterium atpA, G, D, and C genes (coding for the alpha, gamma, beta, and epsilon subunits, respectively) and tested their abilities to complement two uncA (alpha subunit) and two uncD (beta subunit) mutants of E. coli. The results indicated that complementation of either uncD mutant required atpD (beta) only. Complementation of one of the uncA (alpha) mutants required atpA, G, and D (alpha, gamma, and beta) and possibly atpE (epsilon) as well. The other uncA mutant was not complemented by any combination of B. megaterium ATPase genes. Complementation of a beta mutant by atpD (beta) or atpD and C (beta epsilon) produced cells which could grow aerobically on a nonfermentable carbon source (succinate) but not anaerobically on rich medium containing glucose. These E. coli therefore had become obligate aerobes. The ability to grow anaerobically could be restored to the mutant complemented by atpD alone by growth at pH 7.5 or pH 8 in the presence of 0.1 M potassium.

Organization and sequence of the genes coding for the proton-translocating ATPase of Bacillus megaterium.

We have cloned and sequenced the genes for the subunits of the proton-translocating ATP synthase of Bacillus megaterium QM B1551. The arrangement of the genes is identical to the arrangement of the same genes (the unc operon) in Escherichia coli. The genes for the Fo subunits immediately precede the genes for the F1 subunits and are themselves preceded by an open reading frame which codes for a protein similar to the E. coli i protein. In contrast to the E. coli ATPase genes, the transcript for these ATPase genes does not include this open reading frame.