Transcription in bacteriophage F1-infected Escherichia coli. I. Translation of the RNA in vitro

Mutational analysis of an inherently defective translation initiation site

In a reverse of many studies of translational initiation sites, we have explored the basis for the inactivity of an apparently defective initiation site. Gene VII of the filamentous phage f1 has a translational start site with highly unusual functional properties and a sequence dissimilar to a prokaryotic ribosome binding site. The VII site shows no activity in assays of independent initiation, even in a deletion series designed to remove potentially interfering RNA secondary structure. Activity from the VII site is only observed if the site is coupled to a source of translation immediately upstream, but its efficiency is low at a one-nucleotide spacing from the stop codon of the upstream cistron and extremely sensitive to the distance between the stop codon and the gene VII AUG. These and other atypical characteristics of coupling distinguish the VII site from most coupled initiation sites. To identify the pattern of nucleotide substitutions that give the VII site the capacity for independent initiation, a series of designed and random point mutations were introduced in the sequence. Improving the Shine-Dalgarno complementarity from GG to GGAG or GGAGG made activity detectable, but at only low levels. Random substitutions, each increasing activity above background by a small increment, were found at 16 positions throughout the region of ribosome contact. These substitutions lengthened the Shine-Dalgarno complementarity or changed the G and C residues present in the wild-type site to A or T. Significant activity was not observed unless a strong Shine-Dalgarno sequence and a number of the up-mutations were present together. The nature and distribution of the substitutions and their agreement with the known preferences for nucleotides in initiation sites provide evidence that the VII site's major defect is its primary sequence overall. It appears to lack the specialized sequence required to bind free 30 S ribosomes, and thus depends on the translational coupling process to give it limited activity.

Transcription in bacteriophage f1-infected Escherichia coli: RNA synthesized on DNA of deletion mutant PII shows the existence of a two-site terminator

Two different transcripts are synthesized on the DNA of deletion mutant PII of bacteriophage f1 in E. coli cells infected with this miniphage. Both RNA species appear to be primary transcripts and differ by about 100 nucleotides at their 3'OH end. Mapping of these molecules on the miniphage genome suggests that a two-site terminator is active at the end of the I region of transcription of bacteriophage f1.

Initiation and termination signals for transcription in bacteriophage M13

Transcription of the infrequently expressed phage M13 genome domain, comprising genes III, VI, I and IV, has been studied in detail by hybridization and S1-nuclease mapping studies. The contiguous genes III and VI are transcribed via an 1800 nucleotide-long RNA molecule that is initiated at a promoter which overlaps with the Rho-independent termination signal between genes III and VIII. Its synthesis is terminated at a Rho-dependent terminator in the proximal part of gene I. Transcription of gene I is not mediated by an independent promoter but most probably by read-through of RNA-polymerase through this terminator. Transcription of gene IV is accomplished by synthesis of four distinct RNAs of about 1500 to 1680 nucleotides long which are initiated at a promoter located immediately in front of gene IV. Termination of these transcripts is generated at least four different sites located in tandem within the intergenic region between genes IV and II.

Specificity of translational regulation by two DNA-binding proteins

The gene V protein of the filamentous bacteriophages fl, fd and M13, and the gene 32 protein of bacteriophage T4 share the property of binding strongly and co-operatively to single-stranded nucleic acids, especially DNA. Moreover, both are capable of repressing the translation of specific mRNAs (gene 32 protein its own, and gene V protein that of the filamentous phage gene II), both in vivo and in vitro. If the mechanism of repression by either of these proteins were based solely on its ability to bind single strands co-operatively, then the other would be expected to mimic or interfere with its effect in vitro. We have found no such mimicry or interference, even at protein concentrations high enough to have substantial non-specific effects on translation. This suggests that the sites of repression on the mRNAs must offer something other than simple "unstructuredness" for binding and repression to occur.

Transcription in bacteriophage f1-infected Escherichia coli: very large RNA species are synthesized on the phage DNA

Fractionation of pulse-labeled RNA extracted from E. coli cells infected with phage f1 and hybridization of this RNA to f1 DNA reveals that very large species are synthesized on the phage genome. Hybridization of the RNA to specific fragments of f1 DNA shows that, in the infected cell, at least one mRNA is present into which the sequences of genes III, VI, and I are all transcribed together. This result fully explains the polar effect shown by gene III mutants on the expression of genes VI and I (Pratt et al. 1966).

M13 procoat and a pre-immunoglobulin share processing specificity but use different membrane receptor mechanisms

Bacteriophage M13 procoat is accurately processed to transmembrane coat protein by salt-washed or N-ethylmaleimide-treated rough microsomes from dog pancreas. These treatments inhibit the processing of eukaryotic secreted protein precursors. M13 procoat can assemble into dog pancreas microsomes post-translationally. Thus, the microsomal proteins needed for assembly may be determined by the nature of the precursor protein itself. These results, and our finding that the mouse IgG kappa chain fragment precursor is processed by Escherichia coli leader peptidase, also suggest that the cleavage specificity of leader (signal) peptidases and the properties of preproteins that render them suitable for cleavage have been conserved during evolution.

Transcription in bacteriophage f1-infected Escherichia coli. Messenger populations in the infected cell

Transcription of bacteriophage f1 DNA in vivo occurs in two independent regions. They are separated from one another by a strong terminator just downstream from gene VIII on one side, and by the filamentous phage intergenic space on the other. One of these regions contains genes II, V, VII, IX and VIII, and is actively transcribed. In this region there are a number of promoters but only one effective terminator. Thus, most of the RNAs that come from this region overlap and share sequences close to the termination site. The other region, which contains genes III, VI, I and IV, is transcribed much less actively. This region gives rise to a long (approximately 4 X 10(3) bases) RNA that covers the entire region, and several RNAs that overlap in the region closest to their 5' termini. Several other RNAs appear to overlap only with the 4 X 10(3) base transcript. Thus, not only the frequency but the organization of transcription differs in the two portions of the genome.

The replication of bacteriophage f1: gene V protein regulates the synthesis of gene II protein

Two filamentous phage gene products are required for the replication of phage DNA. One of these, the gene II protein, is a site-specific endonuclease required for all phage-specific DNA synthesis. The other, the gene V protein, is a single-stranded DNA-binding protein required only for single-strand synthesis. Purified gene V protein, when added to an in vitro protein synthesizing system programmed by f1 DNA, specifically inhibits the synthesis of gene II protein. Inhibition seems to be translational, since synthesis of gene II protein from an RNA template is also inhibited by gene V protein. Gene V protein control of gene II expression can account for the regulation of the level of expression of the filamentous phage genome.

Membrane assembly from purified components. I. Isolated M13 procoat does not require ribosomes or soluble proteins for processing by membranes

The coat protein of coliphage M13 is an integral protein of the host-cell cytoplasmic membrane prior to its assembly into virions. It is initially synthesized as procoat, a soluble precursor with a 23 amino acid leader sequence at its amino terminus. 35S-labeled procoat accumulates during an in vitro translation reaction that contains 35S-methionine and RNA from M13-infected cells. Radiochemically pure procoat has been isolated from in vitro translation reactions by extraction into an organic solvent and gel filtration through Sephadex LH-60. Radiochemically pure procoat can be used as substrate in rapid and quantitative assays for leader peptidase and for leader peptide hydrolase, an enzyme that degrades the leader peptide after its release from procoat. Procoat solubility, digestion by leader peptidase and processing by membranes are affected by the presence of Mg2+ ion. Isolated procoat is soluble in water at low ionic strength and mildly alkaline pH as well as in detergent solutions. It is cleaved to coat protein by purified E. coli leader peptidase and by inverted E. coli inner-membrane vesicles. These properties of the purified procoat mirror those of the procoat in crude extracts. This suggests that there are no other soluble components that are necessary for the assembly of procoat into the membrane and its conversion to coat; specifically, it provides powerful evidence that protein synthesis is not involved.