Nucleotide sequence of bacteriophage lambda DNA

The nucleotide sequence of the DNA of bacteriophage λ has been determined using the dideoxy chain termination method in conjunction with random cloning in M13 vectors. Various methods were studied for sequencing specific regions to complete the sequence, but all were much slower than the random approach. The DNA in its circular form contains 48,502 base-pairs. Open reading frames were identified and, where possible, ascribed to genes by comparing with the previously determined genetic map. The reading frames for 46 genes were clearly identified, though in about 20 the position of the protein initiation site could not be rigorously established. Probable positions for the kil, cIII and lom genes are suggested but remain uncertain. There are about 20 other unidentified reading frames that may code for proteins.The genome is fairly compact with comparatively little non-coding DNA. In many cases the translation terminators and initiators overlap, particularly in the sequence A-T-G-A where the TGA terminates one gene and the ATG initiates the next. Such structures seem to be characterized by a purine-rich sequence, rather than by a specific “Shine and Dalgarno” sequence, before the initiator. In the whole of the left arm the codon CTA, which is normally read by a minor leucine tRNA, is absent. The distribution of other rare codons in the genes of the left arm suggests that they may have a controlling function on the relative amounts of the proteins produced.     

Nucleotide sequence of bacteriophage fd DNA.

The sequence of the 6,408 nucleotides of bacteriophage fd DNA has been determined. This allows to deduce the exact organisation of the filamentous phage genome and provides easy access to DNA segments of known structure and function.     

Nucleotide sequence of the three major early promoters of bacteriophage T7.

I have determined the nucleotide sequences of the three major early promoters of bacteriophage T7 (A1, A2, A3). The sequences confirm the two main homologies found between other known promoters for E. coli RNA polymerase (nucleoside triphosphate:RNA nucleotidyl transferase, E.C. 2. 7. 7. 6). In particular, all three T7 promoters show a very good match with the -35 region homology; the A2 and A3 promoters share a 17 basepair sequence in this region. On the other hand, the match with the Pribnow Box homology is much less pronounced and different for each T7 promoter.     

Nucleotide sequence of bacteriophage f1 DNA.

The nucleotide sequence of the DNA of the filamentous coliphage f1 has been determined. In agreement with earlier conclusions, the genome was found to comprise 6,407 nucleotides, 1 less than that of the related phage fd. Phage f1 DNA differs from that of phage M13 by 52 nucleotide changes, which lead to 5 amino acid substitutions in the corresponding proteins of the two phages, and from phage fd DNA by 186 nucleotide changes (including the single-nucleotide deletion), which lead to 12 amino acid differences between the proteins of phages f1 and fd. More than one-half of the nucleotide changes in each case are found in the sequence of 1,786 nucleotides comprising gene IV and the major intergenic region between gene IV and gene II. The sequence of this intergenic region (nucleotides 5501 to 6005) of phage f1 differs from the sequence reported by others through the inclusion of additional single nucleotides in eight positions and of a run of 13 nucleotides between positions 5885 and 5897, a point of uncertainty in the earlier published sequence. The differences between the sequence of bacteriophage f1 DNA now presented and a complete sequence for the DNA previously published by others are discussed, and the f1 DNA sequence is compared with those of bacteriophages M13 and fd.     

Nucleotide sequence and genome organization of bacteriophage S13 DNA

The complete sequence of bacteriophage S13 DNA has been determined. The molecule has 5386 nucleotides and differs from φX174 by 87 transitions and 24 transversions. All the proteins, A, A^*, B, C, D, E, F, G, H, J and K found in φX174 are also present in S13. Due to changes in the H/A intergenic region of S 13, the start of an additional protein. A′, has been identified. Genes F and H coding for the capsid and spike proteins, respectively, are the least conserved in comparison to φX174. Many of the silent changes, as well as some amino acid changes, are found in the same nucleotide sequence positions in phage G4, confirming the interrelationship between the three phages.     

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.     

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.