Virus-specific proteins in Escherichia coli infected with some amber mutants of phage MS2

Energy-efficient growth of phage Q Beta in Escherichia coli

The role of natural selection in the optimal design of organisms is controversial. Optimal forms, functions, or behaviors of organisms have long been claimed without knowledge of how genotype contributes to phenotype, delineation of design constraints, or reference to alternative designs. Moreover, arguments for optimal designs have been often based on models that were difficult, if not impossible, to test. Here, we begin to address these issues by developing and probing a kinetic model for the intracellular growth of bacteriophage Q beta in Escherichia coli. The model accounts for the energetic costs of all template-dependent polymerization reactions, in ATP equivalents, including RNA-dependent RNA elongation by the phage replicase and synthesis of all phage proteins by the translation machinery of the E. coli host cell. We found that translation dominated phage growth, requiring 85% of the total energy expenditure. Only 10% of the total energy was applied to activities other than the direct synthesis of progeny phage components, reflecting primarily the cost of making the negative-strand RNA template that is needed for replication of phage genomic RNA. Further, we defined an energy efficiency of phage growth and showed its direct relationship to the yield of phage progeny. Finally, we performed a sensitivity analysis and found that the growth of wild-type phage was optimized for progeny yield or energy efficiency, suggesting that phage Q beta has evolved to optimally utilize the finite resources of its host cells.

A complete plasmid-based complementation system for RNA coliphage Q beta: three proteins of bacteriophages Q beta (group III) and SP (group IV) can be interchanged

Our laboratory has established a bacteriophage Q beta cDNA-containing plasmid system in which virtually all coding defects present within the 4217 nucleotide Q beta genome can be complemented in trans. In this system, Q beta minus strand RNAs are constitutively transcribed from plasmid cDNA by Escherichia coli RNA polymerase. Replication of these minus strands results in the synthesis of Q beta plus RNA, thereby triggering an infectious cycle in which Q beta phase particles are generated. Genetically engineered Q beta genome mutations that result in defective viral proteins can be complemented in trans by the products of one or more Q beta helper plasmids that express either: (1) Q beta maturation protein, which can complement defects in the Q beta maturation cistron (nucleotides 61 to 1320); (2) Q beta readthrough protein, which can complement defects in the readthrough cistron (nucleotides 1344 to 2330); or (3) Q beta replicase, which can complement defects in the replicase cistron (nucleotides 2352 to 4118). Each plasmid component of this system contains a unique origin of replication and carries a different antibiotic gene, thereby enabling all combinations of these plasmids to coexist in the same host. We have further developed a second series of helper plasmids that generate the corresponding viral proteins of the related group IV RNA phage SP. Each of these SP helper proteins can complement respective defects within the Q beta genome with efficiencies similar to those observed for the Q beta helper proteins. It is now possible to supply functional Q beta or SP proteins in trans to examine Q beta genomes that contain protein coding defects for their ability to synthesize Q beta proteins, replicate Q beta RNA, assemble virions, and/or lyse the host cell.

Characterization of Op3, a lysis-defective mutant of bacteriophage f2

We have isolated a conditional lethal mutant of bacteriophage 12 which makes plaques only on E. coli strains carrying a UGA suppressor. It grows normally in nonsuppressing hosts but does not lyse such strains. The mutation complements with amber mutations in each of the three known phage cistrons. These observations lead us to postulate the existence of a fourth gene in the RNA phage.

Non-continuous translation of coat protein and ribonucleic acid polymerase cistrons in MS2 bacteriophage ribonucleic acid

In an MS2 phage ribonucleic acid (RNA)-directed in vitro protein-synthesizing system, the coat protein cistron and the adjacent RNA polymerase cistron are translated non-continuously. The ribosomes which have completed the synthesis of coat protein dissociate from the MS2 RNA and do not read through the intercistronic gap. Translation of the adjacent RNA polymerase cistron requires ribosomes other than those translating the coat protein cistron.

Nucleotide sequence at the binding site for coat protein on RNA of bacteriophage R17

The binding of a few molecules [1-6] of RNA bacteriophage coat protein to 1 molecule of RNA represses in vitro translation of the RNA synthetase cistron. Digestion of the complex, R17 coat protein-R17 RNA, by T1 RNase yields an RNA fragment bound to the coat protein. The nucleotide sequence of this fragment (59 residues) reveals that it contains the punctuation signal between the coat protein and RNA synthetase cistrons, suggesting that this is the site on the RNA where the coat protein acts as a translational repressor.

Fermentation process for double-stranded ribonucleic acid, an interferon inducer

Double-stranded ribonucleic acid (ds-RNA) isolated from Escherichia coli infected with bacteriophage MS2 is a potent interferon inducer. High levels of ds-RNA are formed in nonpermissive cells infected with MU9, an amber coat protein mutant of MS2. This mutant has been used to develop a process for large-scale ds-RNA production. Preparation of quantities of MU9 lysate sufficient for ds-RNA production in fermentors is described. Over 300 mug of ds-RNA/ml can be accumulated after MU9 infection of cultures grown to high density in corn steep liquor medium. This is approximately 300 times the amount of ds-RNA made by MS2 infection of cells grown in tryptone medium. Maximum ds-RNA formation requires only 3 hr. The ds-RNA is stable and remains inside nonaerated cells for at least 17 hr.

Properties of the ribonucleic acid bacteriophage ZIK-1 coat protein and its synthesis in an Escherichia coli cell-free system

The coat protein subunit of the RNA bacteriophage ZIK/1 has a molecular weight of 12100 and does not contain histidine, methionine and cysteine. The amino acid composition of the coat protein is different from that of other RNA bacteriophage coat proteins. Bacteriophage ZIK/1 belongs to a class of RNA bacteriophages distinct from the f2 type, which lack histidine in their coat proteins, and the Qbeta type, which lack histidine and methionine. Bacteriophage ZIK/1 RNA is an efficient template in the Escherichia coli cell-free system producing coat protein as the major product and a number of non-coat proteins. This result is similar to that obtained with RNA from f2-type bacteriophages. It is probable that the genomes of RNA bacteriophages are structurally similar and that differences between the types of RNA bacteriophage arise from minor differences in RNA sequence.

Structure of the poly(G) polymerase component of the bacteriophage f2 replicase

A rifampicin-resistant poly(G) polymerase has been purified from f2 sus 11-infected cells. The poly(G) polymerase is believed to represent part of the f2 replicase on the basis of several criteria. It is present only in infected cells and shares the characteristic rifampicin resistance of crude f2 replicase activity. Partially purified poly(G) polymerase preparations exhibit replicase activity, synthesizing f2 "lus"strand RNA from denatured, partially double-stranded f2 RNA template. Highly purified poly(G) polymerase preparations, although lacking replicase activity, contain a protein which is electrophoretically identical to the protein product of the viral replicase cistron.