Part I. Physico-chemical Principles.- 1. Introduction.- 2. Formation of Primordial Bioorganic Molecules.- 3. Hidden Aspects of Chirality.- 4. RNAs and Their Constituents.- 5. Proteins and Their Constituents.- 6. Membranes.- 7. Compounds Required for Life Part II. Scenarios of Ancient Worlds.- 8. The RNA World Involves RNA as a First Genetic System.- 9. Peptide and Protein World.- 10. Combinations of the RNA with the Peptide World.- 11. The Precellular World of Viruses.- 12. Combinations of Different Worlds.- 13. The Iron Sulfide World of Proto-Metabolism.- 14. The Genetic Code.

A new hypothesis of the ancestors of contemporary viruses, the genovirions is proposed. This concept emphasizes the close connection between the evolution of viruses and the proto-cells. Recent and mounting evidences from comparative genomics indicate that both RNA and DNA viruses evolved from primordial genetic elements before proto-cells existed. The most persuasive discoveries that challenge the conventional virus concept include the giant virusphage Mimivirus, the insect polydnaviruses, some unusual archaeal viruses, and the large phycodnaviruses. The existence of several viral genes central to replication and structure shared with many viruses but not present in cellular genomes indicates that once an ancient virus era existed. As viruses are the only quasi-living beings that use RNA as genetic information and storage carrier, their ancestors were witnesses of the RNA world. The ancient virus scenario existed at the time of the RNA world before proto-cells developed hence these genetic elements were not cell parasites. Later on, retroviruses were responsible for the transition from the RNA to the DNA world.

In an extensive host range study ofM. hyorhinis mink lung cells (MvlLu, ATCC CCL 64) were found to be the cells of choice for the propagation of this mycoplasm, which otherwise is often difficult to grow in a cell-free medium. Furthermore, rapid plaque assay and plaque purification procedures were developed forM. hyorhinis. The titer ofM. hyorhinis grew to 1×107 to 1×108 pfu/ml within three d postinoculation on mink lung cells. DNA restriction enzyme analysis of the genome ofM. hyorhinis was performed. Endonucleases Bst EII and Xho I are the most suitable enzymes for cleavingM. hyorhinis DNA into distinct fragment patterns. Thus, the use of the combination mink lung cells for mycoplasma growth with subsequent restriction enzyme analysis leads to an unamibiguous detection and identification toM. hyorhinis strains even in minute amounts.

Background: Foamy virus Bel1/Tas trans-activators act as key regulators of gene expression and directly bind to Bel1 response elements (BRE) in both the internal and the 5' LTR promoters leading to strong transcriptional trans-activation. Cellular coactivators interacting with Bel1/Tas are unknown to date.Results: Transient expression assays, co-immunoprecipitation experiments, pull-down assays, and Western blot analysis were used to demonstrate that the coactivator p300 and histone acetyltransferase PCAF specifically interact with the retroviral trans-activator Bel1/Tas in vivo. Here we show that the Bel1/Tas-mediated trans-activation was enhanced by the coactivator p300, histone acetyltransferases PCAF and SRC-1 based on the crucial internal promoter BRE. The Bel1/Tas-interacting region was mapped to the C/H1 domain of p300 by co-immunoprecipitation and pull-down assays. In contrast, coactivator SRC-1 previously reported to bind to the C-terminal domain of p300 did not directly interact with the Bel1 protein but nevertheless enhanced Bel1/Tas-mediated trans-activation. Cotransfection of Bel1/Tas and p300C with an expression plasmid containing the C/H1 domain partially inhibited the p300C-driven trans-activation.Conclusions: Our data identify p300 and PCAF as functional partner molecules that directly interact with Bel1/Tas. Since the acetylation activities of the three coactivators reside in or bind to the C-terminal regions of p300, a C/H1 expression plasmid was used as inhibitor. This is the first report of a C/H1 domain-interacting retroviral trans-activator capable of partially blocking the strong Bel1/Tas-mediated activation of the C-terminal region of coactivator p300. The potential mechanisms and functional roles of the three histone and factor acetyltransferases p300, PCAF, and SRC-1 in Bel1/Tas-mediated trans-activation are discussed.

Foamy virus (FV) Bel1/Tas transactivators act as key regulators of gene expression and directly bind DNA Bel1 response elements (BREs) in both the internal (IP) and 5'LTR promoters. Here, we report the mapping and the virus species specificity of the nonhomologous feline foamy virus (FFV) BREs in both promoters. The data indicate that FFV Bel1 did not bind the primate FV IP.BRE and that primate FV Bel1 was not capable of binding the FFV IP.BRE. In addition, we show that the C-terminal activation domain of FFV Bel1 does not contribute to DNA binding because a C-terminal trans-dominant negative FFV Bel1 mutant was still able to bind to both promoters.

Oligopeptides that correspond to proteolytic cleavage site junctions of the native Gag and Pol proteins are specifically cleaved by retroviral aspartate proteases (PRs). The role of the flap subdomain of the PR of the human spumaretrovirus (HSRV) and of substrate peptides in cleavage site specificity was analyzed by site-directed mutagenesis. Native and mutant peptides were subjected to proteolysis by the authentic and mutated recombinant viral enzyme. The results reveal that Glu residue 54 of the HSRV PR is an essential specificity determinant for proteolytic processing of the structural proteins. Peptides that represent in vivo cleavage sites were susceptible to proteolysis by the recombinant HSRV PR, but one peptide located at the junction between the PR and reverse transcriptase domains was completely resistant to cleavage. Thus the data indicate that a proteolytic cleavage between these domains does not occur in vivo. Naturally occurring and mutant forms of the cleavage-resistant peptide were therefore analyzed by circular dichroism to determine if differences existed in the secondary structures of the peptides that did or did not serve as substrates. The data show that differences in the secondary structure of the native and mutant peptides analyzed does not seem to play a crucial role for cleavage site specificity in HSRV PR. Instead highly conserved hydrophobic residues at distinct positions of the HSRV cleavage site junctions contribute to the specificity observed as reported for HIV-1 PR.

The foamy viral proteases (FV PRs) are set apart from other retroviral processing enzymes by unique features. The first remarkable property is that FV PRs are enzymatically active as high-molecular-mass Pro-Pol proteins. Hence there exist multiple forms of active FV PRs that likely contribute to cleavage site specificity. A FV PR of low molecular size is not detectable in purified virions, in contrast to PRs of other retroviruses that are found in virus particles. Because the major part of Pol remains. attached to the amino-terminal enzymatically active PR protein region, the FV-specific way of expressing Pro-Pol polyproteins from a pol-specific transcript provides for the incorporation of Pro-Pol and IN into virus particles. Proteolytic processing of Gag and Pol proteins is incomplete and delayed. Another novel feature is that the catalytic center of the active dimers of cat FV PR consists of D-S/T-Q instead of D-S/T-G, an unprecedented feature of this enzyme. The temporal and spatial control and the factors that regulate FV PRs remain to be elucidated.

Gene expression of the internal and long terminal repeat promoters of the spuma retrovirus is specifically activated by the transactivator Bell, the key regulator of viral gene expression. Bell directly binds to and activates DNA target sites of viral promoters and those of distinct cellular genes. To determine the contribution of cellular transcription factors to viral transactivation, the viral internal promoter (IP) was analyzed by transient expression, electrophoretic mobility shift assays), and supershifts. Here we report that Bell-mediated transactivation of the full-length and shortened versions of the Bell response element (BRE) were repressed by nuclear factor I (NFI). Electrophoretic mobility shift assays using nuclear extracts from transfected 293T cells revealed that different DNA-protein complexes consisting of DNA target sites of NFI and Bell proteins were formed. The specificity of the repressor and transactivator DNA binding was shown by NFI and Bell-specific antibodies that led to supershifts of the different nuclear protein-oligodeoxynucleotide complexes. The specificity of the complexes was confirmed by using unlabeled, shortened, and mutated IP.BRE oligode-oxynucleotides in competition experiments with the authentic IP.BRE. Cotransfection of the infectious spuma-virus DNA genome with a human NFI-X1 expression plasmid into cell cultures greatly reduced the expression of viral structural and Bell proteins. These data demonstrate the relevance of NFl-mediated repression of Bell-driven transactivation in vivo.

Expression of the human cyclin-dependent protein kinase inhibitor p57(Kip2) gene was previously shown to be specifically and strongly activated by the retroviral trans-activator Bel1 of human foamy virus by means of expression profiling, Northern, and Western blot analysis. Here we report that Bel1-mediated trans-activation was conferred by a Bel1 response element (BRE) located in the second exon of p57(Kip2). The intragenic Kip2-BRE was capable of trans-activating the luciferase reporter gene upon cotransfection with Bel1. In electrophoretic mobility shift assays using 293T nuclear extracts or a purified glutathione S-transferase (GST)(.)Bel1 fusion protein, we identified the 55-nucleotide-long Kip2-BRE site that mainly consists of three direct repeats of 14-mers partially homologous to a functionally active ERE in the viral internal promoter. The specificity of the transactivator-DNA binding was shown by using mutated and shortened Kip2-BRE oligodeoxynucleotides in competition experiments with the authentic viral internal promoter and by Bel1-specific antibody that led to a supershift of the nuclear protein(.)Kip2-BRE and GST(.)Bel1(.)Kip2-BRE complex. The data indicate that bel1 can directly bind to BRE sites. The cellular Kip2-BRE can be used to predict those human genes that are directly or indirectly activated by the Bel1 trans-activator.

Foamy viruses (FV) are complex retroviruses with additional bel genes located between env and the 3′ long-terminal repeat. The functions of the bel 2 and bet genes are unknown and both are dispensable for replication of the prototypic human foamy virus in cell cultures. We examined the function(s) of bel 2 and bet of the distantly related feline foamy virus (FFV) in the proviral context. Mutagenesis was used to alter the Bel 2 and Bet or to abrogate their expression. The Bel 2/Bet mutants showed a 1000-fold reduced viral titer in feline kidney cells; in human 293T cells, viral titer was only about 10-fold reduced compared to wild-type FFV. In both cell types, the Bel 2/Bet mutations resulted in a reduced release of FFV particles. The results indicate that FFV Bet is required for efficient virus replication. The functions of the Bel 2 and Bet proteins are discussed.

We have previously demonstrated that 12-O-tetradecanoylphorbol-13-acetate (TPA) activates human T-cell leukemia virus type-I long terminal repeat (LTR) in Jurkat cells by a protein kinase C (PKC)-independent mechanism involving a posttranslational activation of Sp1 binding to an Sp1 site located within the Ets responsive region-1 (ERR-1). By employing the PKC inhibitor, bisindolylmaleimide I and cotransfecting the reporter LTR construct with a vector expressing PKC-alpha, we demonstrated, in the present study, that this effect of TPA was not only independent of, but actually antagonized by, PKC. Electrophoretic mobility shift assays together with antibody-mediated supershift and immuno-coprecipitation analyses, revealed that the posttranslational activation of Sp1 was exerted by inducing the formation of Sp1-p53 heterocomplex capable of binding to the Sp1 site in ERR-1. Furthermore, we demonstrated that Jurkat cells contain both wild-type (w.t.) and mutant forms of p53 and we detected both of them in this complex at variable combinations; some molecules of the complex contained either the w.t. or the mutant p53 separately, whereas others contained the two of them together. Finally, we showed that the Sp1-p53 complexes could bind also to an Sp1 site present in the promoter of another gene such as the cyclin-dependent kinase inhibitor p21(WAF-1), but not to consensus recognition sequences of the w.t. p53. Therefore, we speculate that there might be several other PKC-independent biological effects of TPA which result from interaction of such Sp1-p53 complexes with Sp1 recognition sites residing in the promoters of a wide variety of cellular and viral genes.