Bacteriophage MS2 RNA

A., Volckaert, G., and Ysebaert, M. (1976) Complete nucleotide-sequence of bacteriophage MS2-RNA - primary and secondary structure of replicase gene. Nature, 260, 500-507. 

One of the most striking results that has emerged from the high-resolution crystallographic studies of these icosahedral viruses is that their coat proteins have the same basic core structure, that of a jelly roll barrel, which was discussed in Chapter 5. This is true of plant, insect, and mammalian viruses. In the case of the picornaviruses, VPl, VP2, and VP3 all have the same jelly roll structure as the subunits of satellite tobacco necrosis virus, tomato bushy stunt virus, and the other T = 3 plant viruses. Not every spherical virus has subunit structures of the jelly roll type. As we will see, the subunits of the RNA bacteriophage, MS2, and those of alphavirus cores have quite different structures, although they do form regular icosahedral shells. 

Figure 16.19 Schematic drawing illustrating the structure and sequence of the RNA fragment that is recognized and bound by the coat protein of bacteriophage MS2. The RNA fragment forms a base-paired stem with a bulge at base -10 and a loop of four bases. Bases that form sequence-specific Interactions with the coat protein are red. (Adapted from a diagram provided by L. Llljas.)...

Figure 5.13 The RNA of bacteriophage MS2. The molecule is single stranded but there are extensive regions of complementary bases, so that pairing within the strand leads to the secondary structure shown. Note that the start sites for three coding regions are in the same part of the folded molecule.

Sequencing.—With the elucidation of the primary and secondary structure of the replicase gene, the complete 3569-nucleotide-long sequence of the RNA of bacteriophage MS2 is now known.153 This is the first organism for which theentire nucleic acid structure has been elucidated, and Fiers and his group richly deserve their bouquet. 

Figure 29-17 Partial sequence and secondary structure model of RNA of bacteriophage MS2. The initiation and termination codons for each of the three genes (A protein, coat protein, and replicase) are enclosed in boxes as is the second stop signal that is in-frame for the A protein gene but out-of-frame for the coat protein gene. The entire coat protein gene is shown but less them one-third of the entire sequence is given. From W. Fiers and associates.499-501...

Fig. 7.11. Representation of the high-resolution structure of the bacteriophage MS2 coat protein (magenta) bound to an eighteen nucleotide RNA aptamer (cyan) at 2.8A resolution [112]. The MS2 coat protein is fused to the DBD in the RNAY3H system and is used to anchor the RNA sequence at the promoter region [90],...

Fig. 20. Nucleotide sequence of the three initiation sites of bacteriophages MS2 or R17 RNA. The numbers refer to the T1 oligonucleotides in 2B. (After Revel et aL, 1973)...

Although the 3D structures of RNA aptamers are commonly solved by X-ray crystallography or NMR spectroscopy [44], there are only three reported high resolution structures of RNA aptamers in complex with their targets. These include RNA aptamers in complex with nuclear factor (NF)-kB solved at 2.45 A [45], with bacteriophage MS2 capsid at 2.8 A [46] and with thrombin at 1.8 A resolutions [47]. NF-kB and bacteriophage MS2 capsid naturally bind to nucleic acids. The crystal stmctures of RNA aptamers in complex with the nucleic acid-binding... 

Some E. coli bacteriophages, including f2, MS2, R17, and Qj8, as well as some eukaryotic viruses (including influenza and Sindbis viruses, the latter associated with a form of encephalitis) have RNA genomes. The single-stranded RNA chromosomes of these viruses, which also function as mRNAs for the synthesis of viral proteins, are replicated in the host cell by an RNA-dependent RNA polymerase (RNA replicase). All RNA viruses—with the exception of retroviruses—must encode a protein with RNA-dependent RNA polymerase activity because the host cells do not possess this enzyme. 

The RNA genomes of single-stranded RNA bacterial viruses, such as Q/3, MS2, R17, and f2, are themselves mRNAs. Bacteriophage Q/3 codes for a polypeptide that combines with three host proteins to form an RNA-depen-dent RNA polymerase (replicase). The three host proteins are ribosomal protein SI and two elongation factors for protein synthesis EF-Tu and EF-Ts (see table 28.5). The Q/3 replicase functions exclusively with the Q/3 RNA plus strand template. It first makes a complementary RNA transcript (minus strand) and ultimately uses the minus strand as... 

One of the simplest viruses known is the bacteriophage Qg. It belongs to a class of single stranded RNA phages with very similar properties. The phage MS2 belongs to this family and is a close re-... 

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