Viral genomic RNA

The nonnucleoside reverse transcriptase inhibitors (NNRTIs), used in the treatment of AIDS, provide interesting examples of clinically relevant noncompetitive inhibitors. The causative agent of AIDS, HIV, belongs to a virus family that relies on an RNA-based genetic system. Replication of the vims requires reverse transcription of the viral genomic RNA into DNA, which is then incorporated into the genome of the infected host cell. Reverse transcription is catalyzed by a virally encoded nucleic acid polymerase, known as reverse transcriptase (RT). This enzyme is critical for viral replication inhibition of HIV RT is therefore an effective mechanism for abrogating infection in patients. 

The life history of a retroviras is described in chapter 17 (see Figure 17.45). A summary is presented here. The genome of a retrovirus is composed of RNA not DNA but, when a retrovirus infects a host cell its RNA is transcribed into DNA, catalysed by the enzyme, reverse transcriptase. This DNA is then incorporated into the genome of the host. On transcription of the host DNA, during cell division, viral mRNA and viral genomic RNA are produced. The... 

Wengler, G., Boege, U., Wengler, G., Bischoff, H., and Wahn, K. (1982). The core protein of the alphavirus Sindbis virus assembles into core-like nucleoproteins with the viral genome RNA and with other single-stranded nucleic acids in vitro. Virology 118, 401-410. 

Bioassay-guided fractionation of an aqueous extract from a Philippine Islands collection of the soft coral Lohophytum spp. yielded cembranoid diterpenes, Fig. (3), which exhibited moderate HIV-inhibitory activity in a cell-based in vitro anti-HIV assay [44], while new isomalabaricane triterpenes. Fig. (4), have been isolated from the sponge Stelletta spp. [45]. Other anti-HIV diterpenes also included the dolabellane diterpenes isolated from the Brazilian brown algae Dictyota pfaffi [46] and Dictyota menstrualis [47]. To investigate the effect of these diterpenes in the reverse transcription of the viral genomic RNA, the recombinant HIV-1 RT was assayed in vitro in the presence of each compound. All compounds inhibited the RNA-dependent DNA-polymerase activity of HIV-1 RT and consequently virus replication. 

Most of the viruses that contain DNA (e.g., herpes) use this as a direct template for m-RNA production using host cell DNA-directed RNA-polymerase. However, the pox viruses have their own RNA polymerase. Finally, the so-called retroviruses like HIV use their RNA as a blueprint for the production of a complementary DNA strand with the help of an enzyme called reverse transcriptase - an RNA-dependent DNA polymerase. This nomenclature arises from the fact that these organisms operate in reverse of the normal cellular replicative process whereby DNA acts as a blueprint for RNA production. The DNA thus produced is incorporated into host cell DNA with the help of another viral enzyme - HIV integrase - and the cell ultimately produces new viral genomic RNA and viral proteins using its normal replication procedures. 

There are some exceptions to the norm of DNA-dependent DNA or RNA synthesis, mostly in lower eukaryotes or viruses (Fig. 5). One example is RNA-dependent RNA synthesis in plant, animal, or bacterial viruses. In these cases, a single-stranded RNA template rather than double-stranded DNA guides synthesis of the complementary RNA strand, based on conventional base pairing. The polarity of RNA adds a level of complexity during synthesis. Thus, the RNA genome of a virus that can be directly read and thus provides the mRNA function is called the positive strand, as in polio vims. In this case, the viral genome RNA functions as the mRNA and encodes the RNA polymerase, which is synthesized like other viral proteins in the infected cell. This RNA polymerase subsequently synthesizes the complementary... 

Viral vectors are usually classified by the characteristics of the parental viius. Based on the viral genome, one can distinguish between DNA and RNA viruses (for details see [1, 2]). 

Fig. 1 Antiviral genes inhibit virus replication at different stages of the viral life cycle. Early inhibitors prevent the establishment of the viral genome in the target cell (class I, e.g., entry inhibitors, RT inhibitors for HIV). Intermediate inhibitors prevent viral gene expression or amplification of the viral genome (class II, e.g., siRNAs, antisense RNAs). Late inhibitors prevent virion assembly or release, or inactivate the mature virions (class III, e.g., transdominant core proteins, capsid-targeted virion inactivation, CTVI). A list of antiviral genes in each class is found in Table 1...

Fig. 5.1 Regulators of pre- and post-integration latency. Pre-integration latency is regulated as the viral RNA is reverse transcribed into the proviral DNA (A). This is controlled by the avaUabdity of the nucleotide pool, half life of the forming proviral cDNA copy, and the interaction of the viral protein Vif with the cellular antiviral protein APOBEC, espedaUy family members 3G and 3R It is also regulated at the step of transport across the nuclear membrane through the availability of ATP as the process requires energy (B). Post-integration, the proviral DNA copy of the viral genome, is regulated maiiily by the avadabdity of host transcription factors, especially NF-kB and NFAT (C)...

The viral protein Rev may also play a role in HIV-1 latency. Expression of the viral Rev protein is essential for the nuclear export of genomic RNA as well as unspliced and/or singly spliced transcripts (Cullen 2003), which are ultimately translated into structural, regulatory, and enzymatic viral proteins. Retention of Rev and Tat (viral transactivator proteins) transcripts in the nucleus of resting CD4h- T cells from HAART patients (Lassen et al. 2006) might be involved in the maintenance of post-integration latency in these cells. Importantly, this phenomenon is non-existent in activated T cells. 

A virus-specific RNA RNA polymerase is needed, since the cell RNA polymerase will generally not copy double-stranded RNA (and ribosomes are not able to translate double-stranded RNA either). A wide variety of modes of viral mRNA synthesis are outlined in Figure. By convention, the chemical sense of the mRNA is considered to be of the plus (+) configuration. The sense of the viral genome nucleic acid is then indicated by a plus if it is the same as the mRNA and a minus if it is of oppposite sense. If the virus has double-stranded DNA (ds DNA), then mRNA synthesis can proceed directly as in uninfected cells. However, if the virus has a singlestranded DNA (ss DNA), then it is first converted to ds DNA and the latter serves as the template for mRNA synthesis with the cell RNA polymerase. 

This enzyme is associated with the virions of RNA tumor viruses such as the Rous sarcoma virus (RSV). The enzyme has remarkable enzymatic activity in that it can catalyze several seemingly diverse steps in the synthesis of double-stranded DNA from the single-stranded RNA viral genome. The enzyme uses a tRNA for tryp-tophan as a primer to make a copy of DNA that is complementary to the viral RNA. The resulting RNA-DNA hybrid is converted to a double-stranded DNA molecule by ribon-uclease (RNase)H and DNA-dependent DNA polymerase activities that are intrinsic to reverse transcriptase. 

Genome The total genetic information present in an organism. Viral genomes are unusual in that they can be diverse. Examples of viral genomes include single-stranded DNA, single- and double-stranded RNA molecules. 

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