Nucleotide sequence analysis of DNA. II. Complete nucleotide sequence of the cohesive ends of bacteriophage lambda DNA

At the ends of bacteriophage λ DNA, the 5′-terminated strands are 12 nucleotides longer than the 3′-terminated strands. The complete sequence of deoxynucleotides in both the protruding 5′-terminated single strands of λ DNA has been determined by partial repair and by complete repair followed by sequencing of isolated oligonucleotides. Starting from the 5′-end of the left-hand cohesive end, the 12 nucleotides are in the sequence dpGpGpGpCpGpGpCpGpApCpCpT. The sequence from the right-hand cohesive end is exactly complementary to that from the left-hand end.     

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 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 of the O gene and of the origin of replication in bacteriophage lambda DNA.

The nucleotide sequence of the O gene in bacteriophage lambda DNA is presented. According to two possible initiator codons, the primary structure of the O protein deduced from the DNA sequence consists of 278 or 299 amino acid residues. Structure and function of the O protein--one of the two phage initiator proteins for lambda DNA replication--are discussed in the light of a secondary structure model for the O protein. The central part of the O gene contains a cluster of symmetrical sequences extending over 160 base pairs. The point mutation of the cis-dominant replication mutant ti12 is located in this region.     

Nucleotide sequence analysis of DNA. XI. The 3' terminal sequences of bacteriophage lambda and phi 80 DNA

Two procedures have been developed and applied to the determination of the 3′ terminal sequences of λ DNA and φ80 DNA. In the first procedure, each 3′ terminus was specifically labeled with a single ³²P-nucleotide. Radioactive oligonucleotides of different lengths were obtained by partial pancreatic deoxyribonuclease digestion. From the characteristic mobilities of these oligonucleotides in two dimensional fractionation systems, the 3′ terminal sequence -ACCCGCG for the r-strand and -GGTTACG for the l-strand of λ DNA have been determined. In the second procedure, approximately six nucleotides were removed from each 3′ terminus with exonuclease III, and they were replaced with radioactive nucleotides by partial repair synthesis. After enzymatic digestion and sequence analysis, the above sequences have been confirmed. The 3′ terminal sequences in φ80 DNA are identical to those in λ DNA at least up to the fifth nucleotide from the 3′ ends.     

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 cro-cII-oop region of bacteriophage 434 DNA.

The nucleotide sequence of a 869 bp segment of phage 434 DNA including the regulatory genes cro and cII is presented and compared with the corresponding part of the phage lambda DNA sequence. The 434 cro protein as deduced from the DNA sequence is a highly basic protein of 71 amino acid residues with a calculated molecular weight of 8089. While the cro gene sequences of phage 434 and lambda DNA are very different, the nuleotide sequences to the right of the lambda imm434 boundary show differences only at 11 out of 512 positions. Nucleotide substitutions in the cII gene occur with one exception in the third positions of the respective codons and only one out of several DNA regulatory signals located in this region of the phage genomes is affected by these nucleotide substitutions.     

Effects of DNA sequence non-homology on formation of bacteriophage lambda recombinants.

The presence of DNA sequence non-homologies limits the parental material contribution to the genomes of unduplicated bacteriophage λ recombinants. Crosses involving closely linked markers within the lacZ region of λ plac5 have been carried out under conditions severely limiting DNA synthesis. The presence of density labels distinguishing the parental phage permits an assessment of their material contribution to the lacZ recombinant phage that emerge.When both parents harbor point mutations, the recombinants exhibit a broad range of relative parental DNA contributions, providing support for the proposal that the lacZ⁺ recombinants that are detected under these conditions result from mismatch repair processes acting on heterozygous sites within the long regions of heteroduplex structure present in the products of recombination. The presence of a region of non-homology, either a deletion or an insertion sequence, in one of the parents results in a limitation in the material contribution of that parent to the recombinant products. When both parents carry regions of non-homology, the relative parental contributions to recombinant products are further limited and are confined to the density range expected of the products of double-stranded breakage and joining events within the region separating the two mutational sites. These observations suggest that regions of non-homology are excluded from heteroduplex structures and provide support for a role of branch migration of a Holliday (1964) structure in the formation of the heteroduplex regions that are present in the products of recombination.     

Nucleotide sequence of the chi recombinational hot spot chi +D in bacteriophage lambda.

Chi sites in bacteriophage lambda stimulate recombination promoted by the RecBC pathway of Escherichia coli. Mutations which create these sites occur at four widely separated loci in lambda. We report here the nucleotide sequence surrounding the site of one of these loci, chi D, located near the S gene. The mutations creating the active Chi site, designated chi +D, are transversions from CG to AT. This mutation, like the chi +B and chi +C mutations previously analyzed, leads to a nucleotide sequence common to all three active chi sites.     

178-Nucleotide sequence surrounding the cos site of bacteriophage lambda DNA.

A nucleotide sequence of 61 nucleotides at the left end and 117 nucleotides at the right end of DNA from bacteriophage lambdacI857Sam7 was determined by the Maxam and Gilbert method. A perfect inverted repeat sequence of 10 nucleotides is near the left end, and one of 15 nucleotides is near the right end. DNA from another closely related lambda strain, lambdacI857prm116Sam7, has about 10% divergence in the sequence of the first 110 nucleotides at the right end and has a 17-member perfect inverted repeat sequence.     

Nucleotide sequence of a secondary attachment site for bacteriophage lambda on the Escherichia coli chromosome.

The nucleotide sequence of a secondary attachment site for bacteriophage lambda was determined in a region near the rrnB gene at 88 min on the E. coli chromosome. The sequence has a 8 base pair interrupted homology GCT TTTTA to the common core of the primary attachment site (attB) and the corresponding phage sequence (attP). The site of crossover during integration lies probably between nucleotides -3 and +1. The flanking regions have no obvious homology to the arms of either attP or attB.     

DNA sequence at the end of the cI gene in bacteriophage lambda.

The nucleotide sequence of 57 base pairs near the end of the cI gene in phage lambda is presented. This sequence was determined by direct sequencing techniques and includes the codons for 11 carboxyterminal aminoacids of the cI product, the lambda repressor. The sequence reveals that the cI gene, which has recently been shown to have a unique initiation region, is terminated by a UGA codon. A GUG triplet, which could act as a translation start signal for the rex gene occurs 8 base pairs beyond the cI termination codon. This GUG triplet is preceded by a sequence that could serve as a strong ribosome binding site for the rex message.     

Nucleotide sequence analysis of DNA. XII. The chemical synthesis and sequence analysis of a dodecadeoxynucleotide which binds to the endolysin gene of bacteriophage lambda

We have selected and chemically synthesized a dodecadeoxynucleotide which is nearly or completely complementary to a defined region of the endolysin gene of bacteriophage λ. The nucleotide sequence of the synthetic dodecanucleotide is determined and confirmed by using two independent methods which involve partial enzymatic hydrolysis followed by end-labeling techniques and two-dimensional “homochromatography.” This dodecanucleotide was found to bind to exonuclease III-treated λDNA and it can be used as a primer for the incorporation of deoxynucleotides to its 3′-end. In the presence of labeled dATP and DNA polymerase I, two molecules of dAMP were incorporated to the end of this primer which is expected if the primer binds to the λDNA specifically at the predicted site on the endolysin gene.