The nucleotide sequence between genes 31 and 30 of bacteriophage T4

Transcription and RNA processing during expression of genes preceding DNA ligase gene 30 in T4-related bacteriophages

Early gene expression in bacteriophage T4 is controlled primarily by the unique early promoters, while T4-encoded RegB endoribonuclease promotes degradation of many early messages contributing to the rapid shift of gene expression from the early to middle stages. The regulatory region for the genes clustered upstream of DNA ligase gene 30 of T4 was known to carry two strong early promoters and two putative RegB sites. Here, we present the comparative analysis of the regulatory events in this region of 16 T4-type bacteriophages. The regulatory elements for control of this gene cluster, such as rho-independent terminator, at least one early promoter, the sequence for stem-loop structure, and the RegB cleavage sites have been found to be conserved in the phages studied. Also, we present experimental evidence that the initial cleavage by RegB of phages TuIa and RB69 enables degradation of early phage mRNAs by the major Escherichia coli endoribonuclease, RNase E.

Identification of two middle promoters upstream DNA ligase gene 30 of bacteriophage T4

Bacteriophage T4 DNA ligase gene 30 lies in the cluster of prereplicative genes located counterclockwise from map units 149 to 121. Based on the early transcription studies this gene has been considered as a typical early gene of bacteriophage T4. In agreement with this assignment, two strong T4 early promoters, P(E )30.8 (128.6) and P(E )30.7 (128.2), located about 3.1 and 2.7 kb upstream from gene 30 have been revealed by promoter mapping and sequence analysis. In addition, the existence of a putative early promoter just upstream of gene 30 was proposed from the sequence data. However, here we show that the putative early promoter just upstream of gene 30 is, in fact, a T4 middle promoter. Furthermore, we detected one more middle promoter located in the genomic region between early promoter P(E )30.7 (128.2) and DNA ligase gene 30 in the coding region of gene 30.3. Both new middle promoters have differences from the consensus MotA box, while their -10 regions match the sigma(70) consensus sequence very well. The 5' ends of MotA-dependent transcripts directed from these promoters, as well as the kinetics of 5' end accumulation in the cells, have been determined by primer extension analysis. The results of these analyses indicate that both MotA-dependent and MotA-independent promoters control the transcription of T4 DNA ligase gene 30 in vivo. Moreover, we show that the first transcripts for gene 30 are directed from its own middle promoter, P(M)30.

A rare type of overlapping genes in bacteriophage T4: gene 30.3' is completely embedded within gene 30.3 by one position downstream

We have previously proposed the existence of one of the rarest types of overlapping genes in bacteriophage T4. We now present the results demonstrating that in a pair of T4 overlapping genes, 30.3 and 30.3', the smaller gene, 30.3', is entirely enclosed within the other by one position downstream. We have constructed plasmids in which different open reading frames from the gene 30.3 region were fused with the 5' end of the lacZ beta-galactosidase (betaGal) gene of Escherichia coli. The gene fusions have been obtained at the position of a HindIII site which was introduced just upstream from the stop codon of gene 30.3'. High betaGal activities have been estimated in the case of plasmids carrying 30.3::lacZ and 30.3'::lacZ fusions. The apparent molecular weights of the fusion proteins, the determined N-terminal sequences, as well as the detected betaGal activities, confirm the structure and arrangement of out-of-phase overlapping genes 30.3 and 30.3'.

Cloning and expression of genes from the genomic region between genes cd and 30 of bacteriophage T4

Ten open reading frames (ORFs) from the cd-30 region of bacteriophage T4, as well as genes 31 and rIII, have been cloned, and all were found to be expressed in a T7 RNA polymerase system. Expression data confirm the existence of genes 31.2, 31.1, 31, rIII, 30.9, 30.8, 30.7, 30.6, 30.5, 30.4, 30.3 and 30.2, which predict peptides of 78, 102, 111, 82, 58, 110, 121, 95, 65, 68, 152 and 278 amino acids (aa), respectively. The major product of gene 30.9 is a basic peptide initiated at the second AUG codon that is found 42 nucleotides downstream and in frame from the first AUG. A plasmid carrying gene 30.3 expresses two different peptides, one of which is of the size predicted for gp30.3. By site-directed mutagenesis we have shown that the smaller peptide is encoded by gene 30.3' which is completely embedded within gene 30.3, but in a different reading frame. Gene 30.3' encodes a 75-aa basic peptide with its C terminus rich in charged aa.