RNA, single-stranded

The N-terminal part of the tomato bushy stunt virus polypeptide chain (the R-segment in Figure 16.8) is disordered in all the subunits. As in the core of many other single-strand RNA viruses this region of the polypeptide chain... 

The fact that spherical plant viruses and some small single-stranded RNA animal viruses build their icosahedral shells using essentially similar asymmetric units raises the possibility that they have a common evolutionary ancestor. The folding of the main chain in the protein subunits of these viruses supports this notion. 

The human immunodeficiency vims (HIV) is the causative agent of the acquired immunodeficiency syndrome (AIDS). HIV is a retrovirus, whose replication includes the transcription of the single-stranded RNA genome into double stranded DNA (reverse transcription) and the covalent insertion of the DNA... 

Figure 35-7. Diagrammatic representation of the secondary structure of a single-stranded RNA molecule in which a stem loop, or "hairpin," has been formed and is dependent upon the intramolecular base pairing. Note that A forms hydrogen bonds with U in RNA.

HCV is a small enveloped single-stranded RNA virus belonging to the Flaviviridae family and Hepacivirus genus [12]. Other Flaviviridae members include the flaviviruses such as yellow fever virus, and pestiviruses, which are responsible, for example, for bovine viral diarrhea [13]. The most closely related virus identified to date is GBV-B, which infects the tamarind, a new world monkey. GBV-B has also been tentatively classified as a Hepacivirus... 

Hepatitis C, first known as non-A, non-B hepatitis, is a blood-borne infection that is a single-stranded RNA virus belonging to the Flaviviridae family and the Hepacivirus genus.12 The... 

After the virus has attached to CD4 and chemokine receptors, another viral glycoprotein (gp41) assists with viral fusion to the cell and internalization of the viral contents. The viral contents include single-stranded RNA, an RNA-dependent DNA polymerase (also known as reverse transcriptase), and other enzymes. Using the single-stranded viral RNA as a template, reverse transcriptase synthesizes a complementary strand of DNA. The single-stranded viral RNA is removed from the newly formed DNA strand by ribonuclease H, and reverse transcriptase completes the synthesis of double-stranded DNA. The... 

HCV is a single-stranded RNA virus of the Flaviviridae family. It has a 9.4-kb positive-sense genome encoding a polyprotein precursor of 3011 amino acids. Individual isolates of HCV consist of closely related yet heterogeneous populations... 

We have also noted in Section 5.8 that the RNA of the cell is generally in the single-stranded configuration. Interestingly, although single-stranded RNA viruses are more common, viruses are known in which the RNA is in the double-stranded form. 

A number of bacterial viruses have RNA genomes. The best-known bacterial RNA viruses have single-stranded RNA. Interestingly, the bacterial RNA viruses known in the enteric bacteria group infect only bacterial cells which behave as gene donors (males) in genetic recombination. This restriction to male bacterial cells arises because these viruses infect bacteria by attaching to male-specific pili. Since such pili are absent on female cells, these RNA viruses are unable to attach to the females, and hence do not initiate infection in females. 

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. 

Similarly, the case for monophyly is hard to sustain for the origin of multicomponent (segmented) RNA viruses (positive single stranded RNA viruses, e.g. tobravirus, cucumovirus and bromovirus) and plant bipartite DNA viruses (single stranded DNA viruses, e.g. geminivirus) where coinfection ( two for one ) is required for the production of new virions (see Summary in Shostak, 1999). 

Both dogmas had to be revised or expanded, the first because of the discovery of reverse transcriptase (an RNA-dependent DNA-polymerase) by D. Baltimore (MIT) and H. M. Temin (University of Wisconsin). This is an enzyme which catalyses the synthesis of DNA from single-strand RNA ... 

As early as 1972, Kuhn described a model in which he assumed that RNA replication with a certain error rate could have occurred without the participation of enzymes. Natural phenomena with cyclic behaviour are an important factor in Kuhn s thinking these drive duplication processes. Examples are summer and winter, day and night, or high and low tide (whereby the latter were probably subject to greater variations on the primeval Earth than they are today). These rhythms were often linked with considerable temperature variations, which, for example, made possible the transition from double to single strand RNA (and vice versa). It can be assumed that the cyclic variations involved reactions in which monomers were linked to form polymers. 

Completely different mechanisms are involved in the self-assembly of the tobacco mosaic virus (TMV). This virus consists of single-strand RNA, which is surrounded by 2,130 identical protein units, each of which consists of 158 amino acid residues. A virus particle, which requires the tobacco plant as a host, has a rodlike structure with helical symmetry ( Stanley needles ). It is 300 nm long, with a diameter of 18nm. The protein and RNA fractions can be separated, and the viral... 

The sole biochemical function of 2 -5A (and hence 2 -5 A synthetase) appears to be as an activator of a dormant endo-RNase, which is expressed constitutively in the cell. This RNase, known as RNase L or RNase F, cleaves all types of single-stranded RNA (ssRNA). This inhibits production of both viral and cellular proteins, thus paralyzing viral replication. Presumably, cellular destruction of the invading ssRNA will be accompanied by destruction of any additional viral components. Removal of dsRNA would facilitate deactivation of the endo-RNase, allowing translation of cellular mRNA to resume. A 2-5 phosphodiesterase represents a third enzymatic... 

Nuclease PI is another trizinc enzyme which cleaves the phosphodiester bond in single-stranded RNA and DNA. Protein crystallography has revealed that the structure of the three zinc site is very similar to that... 

Several zinc enzymes that catalyse the hydrolysis of phosphoesters have catalytic sites, which contain three metal ions in close proximity (3-7 A from each other). These include (Figure 12.11) alkaline phosphatase, phospholipase C and nuclease PI. In phospholipase C and nuclease PI, which hydrolyse phosphatidylcholine and single-stranded RNA (or DNA), respectively, all three metal ions are Zn2+. However, the third Zn2+ ion is not directly associated with the dizinc unit. In phospholipase C, the Zn-Zn distance in the dizinc centre is 3.3 A, whereas the third Zn is 4.7 and 6.0 A from the other two Zn2+ ions. All three Zn2+ ions are penta-coordinate. Alkaline phosphatase, which is a non-specific phos-phomonoesterase, shows structural similarity to phospholipase C and PI nuclease however,... 

Replication of Viral Nucleic Acid. In addition to producing molecules for the formation of new capsids, the virus must replicate its nucleic acid to provide genetic material for packaging into the capsids. The way in which this is done might vary. In positive-sense, single-strand RNA viruses, a polymerase translated from viral mRNA produces negative-sense RNA from the positive-sense template which is then repeatedly transcribed into more positive strands. 

Gene expression and DNA replication are compared in Table I-l-l. Transcription, the first stage in gene expression, involves transfer of information found in a double-stranded DNA molecule to the base sequence of a single-stranded RNA molecule. If the RNA molecule is a messenger RNA, then the process known as translation converts the information in the RNA base sequence to the amino add sequence of a protein. 

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