The cloning of a T4 transfer RNA gene cluster

Bacteriophage T4 deoxynucleotide kinase: gene cloning and enzyme purification

Gene 1 of bacteriophage T4 has been cloned into a lambda pL expression vector, resulting in the overproduction of deoxynucleotide kinase. A procedure that includes affinity chromatography on Cibacron Blue F3GA-agarose has been used to purify milligram quantities of enzymes from a 2-liter culture. The enzyme has been partially characterized in vitro and in vivo, and it appears to be identical to the deoxynucleotide kinase isolated from T4-infected Escherichia coli. These results prove the earlier contention that the phosphorylation of three dissimilar deoxynucleotides (5-hydroxymethyldeoxycytidylate, dTMP, and dGMP), to the exclusion of most others, is catalyzed by a single protein.

The cloning and expression of transfer RNA gene cluster of Vibrio eltor phage e4

Vibrio eltor phage e4 codes for five different tRNA species (S. Chattopadhyay and R. K. Ghosh, 1988, Virology, 165, 606-608). The tRNA genes contained in a 3.4-kb KpnI fragment (S. Chattopadhyay and R. K. Ghosh, 1988, Virology, 162, 337-345) have been cloned in pUC 19 at the KpnI site. Two recombinant plasmids, pSR216 and pSR112, produced four of the five tRNA species (arginine, isoleucine, tyrosine, and tryptophan) encoded in the phage genome. The tRNA genes were located on a 1.45-kb KpnI-HindIII subfragment.

Nucleotide sequence and analysis of the 58.3 to 65.5-kb early region of bacteriophage T4

The complete 7.2-kb nucleotide sequence from the 58.3 to 65.5-kb early region of bacteriophage T4 has been determined by Maxam and Gilbert sequencing. Computer analysis revealed at least 20 open reading frames (ORFs) within this sequence. All major ORFs are transcribed from the left strand, suggesting that they are expressed early during infection. Among the ORFs, we have identified the ipIII, ipII, denV and tk genes. The ORFs are very tightly spaced, even overlapping in some instances, and when ORF interspacing occurs, promoter-like sequences can be implicated. Several of the sequences preceding the ORFs, in particular those at ipIII, ipII, denV, and orf61.9, can potentially form stable stem-loop structures.

Sequence organization and control of transcription in the bacteriophage T4 tRNA region

Bacteriophage T4 contains genes for eight transfer RNAs and two stable RNAs of unknown function. These are found in two clusters at 70 X 10(3) base-pairs on the T4 genetic map. To understand the control of transcription in this region we have completed the sequencing of 5000 base-pairs in this region. The sequence contains a part of gene 3, gene 1, gene 57, internal protein I, the tRNA genes and five open reading frames which most likely code for heretofore unidentified proteins. We have used subclones of the region to investigate the kinetics of transcription in vivo. The results show that transcription in this region consists of overlapping early, middle and late transcripts. Transcription is directed from two early promoters, one or two middle promoters and perhaps two late promoters. This region contains all of the features that are seen in T4 transcription and as such is a good place to study the phenomenon in more detail.

Initiation of transcription by bacteriophage T4-modified RNA polymerase independently of host sigma factor

After infection of Escherichia coli with bacteriophage T4 a series of modifications of RNA polymerase takes place including the association of several small polypeptides. We isolated RNA polymerase from cells abortively infected with a series of T4 mutants which arrest phage development at different stages and found that different sets of associated proteins are present in RNA polymerase in each case. The patterns of associated polypeptides seem to correlate with DNA content in the infected cells, suggesting that some of them can be involved both in DNA replication and in the transcription apparatus. One of the modified forms of RNA polymerase contains stoichiometric amounts of a protein with Mr = 25,000 (25K protein), which remains associated with the core enzyme after the removal of sigma factor by chromatography on phosphocellulose. The 25K protein was purified to homogeneity and its effect on transcription selectivity was analyzed in an in vitro system using fragments of T4 DNA as templates. The 25K protein exists in two functional forms which direct core RNA polymerase to utilize two different types of transcription start sites (class I and class II promoters). Both activities do not require host sigma factor. The two forms of 25K protein seem to compete with each other for the core enzyme. The isolated 25K protein can form stable dimers, suggesting that its two activities are associated with the dimeric and monomeric forms. Class I (but not class II) promoters can also be utilized in response to the host sigma factor.(ABSTRACT TRUNCATED AT 250 WORDS)

Changed promoter specificity and antitermination properties displayed in vitro by bacteriophage T4-modified RNA polymerase

A 5.5 X 10(3) base-pair fragment of bacteriophage T4 DNA carrying genes 1, 3, 57, ipI and a cluster of transfer RNA genes was used as template for RNA polymerase isolated from uninfected Escherichia coli and from T4-infected bacteria. RNA transcripts were fractionated by gel electrophoresis and mapped by using as transcription template the 5.5 X 10(3) base fragment cleaved with different restriction enzymes. The comparison of the transcripts synthesized by the two RNA polymerases revealed a dramatic difference in their initiation specificities and abilities to utilize a transcription termination site. The T4-modified polymerase utilizes three new promoters on the template DNA fragment that are not utilized by the host enzyme. The modified enzyme, however, fails to produce some of the transcripts synthesized by the host RNA polymerase. The ability of T4-modified RNA polymerase to terminate transcription at a terminator present in the template DNA fragment is greatly reduced as compared to the unmodified host enzyme. The factors responsible for the new initiation and termination properties are associated with RNA polymerase core component. Analysis of RNA polymerase from bacteria infected with T4 mutants demonstrates that the new promoter specificity and the antitermination effect are caused by different factors.

T4-induced antipolarity: temporal heterogeneity in response of early transcription units

When T4 infects Escherichia coli in the absence of protein synthesis, rho-mediated termination takes place on early polycistronic transcription units. During the early period of development, the appearance of delayed early transcripts becomes insensitive to the inhibition of protein synthesis. In the absence of the T4 gene product mot, an inducer for the middle mode of transcription, only the early polycistronic messengers are synthesized. In mot- -infected cells, the synthesis of the distal transcripts still becomes completely insensitive to the polar effect of chloramphenicol. This happens because potential rho-sensitive termination sites are not used in these cells. In this respect, overcoming polarity induced by chloramphenicol can be called a process of antitermination. The mot-independent antitermination can be studied by addition of chloramphenicol during infections with mot- bacteriophage. The effect is stable; it allows a constant percentage of rho-sensitive termination sites in the cell to be traversed by RNA polymerase for at least 10 min at 42 degrees C. By examining six different transcription units on the T4 genome, we find that each transcription unit has a cis-acting component (or components) which determines when its rho-sensitive termination site stops functioning. In extreme cases, rho acts with 100% efficiency in some transcription units, whereas it is almost inactive in others.

Biosynthesis of chloroplast transfer RNA in a spinach chloroplast transcription system

We have developed a chloroplast in vitro transcription system capable of transcribing tRNA genes (trn) from the spinach and Euglena gracilis chloroplast genomes. The RNA polymerase contained in the chloroplast extract transcribes the spinach chloroplast trnM2, trnV1, and trnl1 loci and the trnV1-trnN1-trnR1-trnL1 cluster in the EcoG fragment of the Euglena chloroplast genome. Restriction enzyme modified templates were used to demonstrate that the tRNA genes are transcribed in vitro. RNA fingerprint analysis confirmed that tRNAMetm, tRNAlle1 and tRNALeu are correctly processed transcripts from the spinach chloroplast trnM2, trnl1, and Euglena trnL1 loci respectively. CCAOH is added to the mature tRNAs in vitro by a 3' nucleotidyl transferase present in the chloroplast extract. Deletion mutants were constructed from the trnM2 locus to evaluate the role of 5' flanking sequences in transcription initiation and processing. DNA sequences between positions -56 to -85 upstream of the trnM2 locus are required for maximal transcription of tRNAMetm, but are not essential for processing. The RNA polymerase involved in chloroplast trn transcription is distinguishable from the RNA polymerase isolated as a DNA-protein complex from spinach chloroplast that is active in rRNA transcription.

Nucleotide sequence of the bacteriophage T4 gene 57 and a deduced amino acid sequence

A 693 basepair cloned fragment of bacteriophage T4 DNA, which supports specifically growth of T4 amber mutants in gene 57, has been sequenced. A polypeptide can be deduced from this sequence, that is either 54 or 60 amino acids long depending which of two AUG codons, 18 nucleotides apart, are used for initiation. The size of this deduced polypeptide is compatible with the size of a single polypeptide (based on polyacrylamide gel electrophoresis) synthesized in vivo in E. coli under the direction of the cloned T4 DNA fragment.

Dual function transcripts specifying tRNA and mRNA

A cluster of four tRNA genes in Escherichia coli is co-transcribed with an adjacent gene encoding elongation factor Tu. The resultant transcript that specifies both structural (tRNA) and informational (mRNA) RNA may not be an uncommon occurrence and has interesting regulatory implications.

Assembly of bacteriophage T4 tail fibers: identification and characterization of the nonstructural protein gp57

Formation of both the tail fiber and the baseplate of bacteriophage T4 depends on the product of T4 gene 57. A single amber mutation in that gene causes loss of two T4-specific proteins. Their molecular weights are 18,000 and about 6,000, respectively, based on their electrophoretic mobilities in SDS-polyacrylamide gels. E. coli carrying a cloned T4 DNA fragment of about 700 basepairs, which directs the synthesis of the smaller protein only, specifically supports the growth of gene 57 amber mutants. We conclude that the small protein is a functional product of gene 57.

Control of promoter utilization by bacteriophage T4-induced modification of RNA polymerase alpha subunit

After infection of Escherichia coli cells, bacteriophage T4 induces several changes in the host DNA-dependent RNA polymerase. A well-characterized chemical change is a two-step ADP-ribosylation of the enzyme's alpha subunit (1). In order to investigate the effect of this change on RNA polymerase transcriptional properties in an in vitro system, we have reconstituted the enzyme from separated individual subunits which were obtained from normal or T4-modified RNA polymerases. It is demonstrated that the enzymes containing T4-modified alpha differ from the enzymes with normal alpha in two respects: (i) their overall activity on T4 DNA is reduced and (ii) they fail to utilize certain T4 promotors while efficiently utilizing other promoters. Among the promoters which are switched off by alpha modification are the two promoters of the D region and one of the two promoters of the T4 tRNA gene cluster. The differential effect of alpha modification on the expression of the tRNA and the D regions in vitro correlates with the previously established pattern of their transcription in vivo. It is suggested that the T4-induced ADP-ribosylation of RNA polymerase alpha subunit is involved in the shutoff of the early bacteriophage genes at the late stage of phage development.

IN vitro transcription of bacteriophage T4 tRNA gene cluster from two different promoters

Analysis of primary transcripts made by Escherichia coli RNA polymerase on T4 DNA containing an intact or partially deleted tRNA gene cluster demonstrates that the T4 tRNA genes are transcribed from two promoters differing in their strength. The stronger (P1) and the weaker (P2) promoters are located at distances of 1 kb and 1.5 kb from the tRNA genes, respectively. Selective initiation of individual transcripts with dinucleotides shows that P1 and P2 promoters contain the sequences TAT and CAC respectively. The two-promoter organisation of the tRNA cluster may reflect two superimposed mechanisms of gene expression in T4-infected bacteria.

An Escherichia coli endonuclease responsible for primary cleavage of in vitro transcripts of bacteriophage T4 tRNA gene cluster

An endonuclease activity was isolated from 100,000 g supernatant fraction of Escherichia coli using in vitro primary transcripts of T4 tRNA gene cluster as assay substrates. The endonuclease cleaves the polycistronic RNA precursors into fragments containing monomeric and dimeric stable RNA sequences. The result strongly suggest that this enzyme participates in the early steps of T4 tRNA maturation pathway preceding the action of RNase P.

Transcriptional control of two gene subclusters in the tRNA operon of bacteriophage T4

In bacteriophage T4 DNA, transcription units recognized in vitro by host RNA polymerase consist of promotor-proximal 'immediate early' (IE) genes and promotor-distal 'delayed early' (DE) genes separated from each other by rho-dependent transcription terminators. In vivo, the transition from IE to DE transcription requires phage-specific protein synthesis and can be prevented by chloramphenicol (CAM). Most of the information about IE/DE transition has been obtained by hybridizaton analyses of mixtures of RNA species synthesized simultaneously on several T4 transcription units (for review see ref. 3). A useful model for the study of T4 gene expression at the level of primary transcripts and individual gene products is provided by the T4 tRNA operon, a cluster of genes coding for eight T4-specific transfer RNAs and two stable RNAs (species 1 and 2) of unknown function (Fig. 1). The 10 genes of the tRNA operon are arranged in two subclusters (I and II) with a promotor located about 1 kilobase pair upstream. The primary transcripts and the final gene products of this region have been identified and isolated. Moreover, this genetic region was recently cloned and a part of it sequenced. We describe here the expression of T4 tRNA genes in vivo and in vitro in terms of the IE/DE concept and demonstrate that the two subclusters of the tRNA operon are subject to different modes of control.