The 3'-terminal nucleotide sequences of bacteriophage lambda DNA

Advances in sequencing technology

Faster sequencing methods will undoubtedly lead to faster single nucleotide polymorphism (SNP) discovery. The Sanger method has served as the cornerstone for genome sequence production since 1977, close to almost 30 years of tremendous utility [Sanger, F., Nicklen, S., Coulson, A.R, DNA sequencing with chain-terminating inhibitors, Proc. Natl. Acad. Sci. U.S.A. 74 (1977) 5463-5467]. With the completion of the human genome sequence [Venter, J.C. et al., The sequence of the human genome, Science 291 (2001) 1304-1351; Lander, E.S. et al., Initial sequencing and analysis of the human genome, Nature 409 (2001) 860-921], there is now a focus on developing new sequencing methodologies that will enable "personal genomics", or the routine study of our individual genomes. Technologies that will lead us to this lofty goal are those that can provide improvements in three areas: read length, throughput, and cost. As progress is made in this field, large sections of genomes and then whole genomes of individuals will become increasingly more facile to sequence. SNP discovery efforts will be enhanced lock-step with these improvements. Here, the breadth of new sequencing approaches will be summarized including their status and prospects for enabling personal genomics.

Identification and characterization of phage-resistance genes in temperate lactococcal bacteriophages

The sie2009 gene, which is situated between the genes encoding the repressor and integrase, on the lysogeny module of the temperate lactococcal bacteriophage Tuc2009, was shown to mediate a phage-resistance phenotype in Lactococcus lactis against a number of bacteriophages. The Sie2009 protein is associated with the cell membrane and its expression leaves phage adsorption, transfection and plasmid transformation unaffected, but interferes with plasmid transduction, as well as phage replication. These observations indicate that this resistance is as a result of DNA injection blocking, thus representing a novel superinfection exclusion system. A polymerase chain reaction (PCR)-based strategy was used to screen a number of lactococcal strains for the presence of other prophage-encoded phage-resistance systems. This screening resulted in the identification of two such systems, without homology to sie2009, which were shown to mediate a phage-resistance phenotype similar to that conferred by sie2009. To our knowledge, this is the first description of a phage-encoded super-infection exclusion/injection blocking mechanism in the genus Lactococcus.

Separate sites for binding and nicking of bacteriophage lambda DNA by terminase

The cohesive end site (cos) is the site of action of bacteriophage lambda terminase, the enzyme that introduces staggered nicks to generate the 12-base cohesive ends of mature lambda DNA. Deletion mutations that remove the lambda cohesive end sequence have been isolated after in vitro mutagenesis. The deletions were obtained by digesting the DNA of a cos duplication phage with S1 nuclease to remove the cohesive ends and adjacent base pairs, followed by blunt end ligation and DNA packaging into phage particles. cos2 is the result of a 22-base-pair deletion that exactly removes the segment of rotational symmetry that includes the cohesive end sequence. The cos2 mutation abolishes nicking by terminase but does not affect terminase binding. We conclude that cos contains two sites that interact with terminase: cosN, the nicking site; and cosB, a binding site for terminase.

Bacteriophage lambda DNA packaging: scanning for the terminal cohesive end site during packaging

Bacteriophage lambda packages the DNA of the related phage 21 poorly [Hohn, B. (1975) J. Mol. Biol. 98, 93--106]. To understand the nature of the packaging defect, the interaction of the cohesive end site (cos) specific for phage 21 (cos phi 21) with phage lambda terminase has been investigated. The ability of lambda terminase to cleave cos phi 21 was studied in vitro; lambda terminase cleaved cos phi 21 only 1% as well as it cleaved the phage lambda cohesive end site (cos lambda). In vitro packaging experiments showed that the lambda and 21 packaging specificities observed in vivo are also found in vitro. The cos cleavage reaction was modified so that competition experiments could be performed; these experiments showed that cos phi 21 was unable to bind lambda terminase, thus identifying the nature of the defect. Previous work [Feiss, M., Fisher, R. A., Siegele, D. A., Nichols, B. P. & Donelson, J. E. (1979) Virology 92, 56--67] has shown that the base pairs giving lambda or 21 packaging specificity are at the left end of the chromosome, outside the 22-base-pair symmetry region that includes the annealed cohesive ends. Therefore, terminase binding to cos requires interactions with base pairs to the Nu1 side of the cohesive end symmetry segment. The evidence supports the proposition that cos consists of adjacent sites for binding of terminase and for nicking by terminase. Because cos phi 21 can be cut by lambda terminase to terminate DNA packaging, it is proposed that the terminase that binds and nicks at the initial cos site is brought into contact with the terminal cos site by the packaging process. Terminase recognizes and nicks the cohesive end sequence of the terminal cos without requiring the binding site.

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.

Transposable genetic elements and plasmid evolution

Transposable elements of DNA that are structurally defined and genetically discrete units seem to have an important role in the evolution of bacterial plasmids. Recombination occurring at the termini of such elements can result in the joining together of unrelated DNA segments that lack extensive nucleotide sequence homology. In addition, transposable elements serve as novel biological switches capable of turning on and off the expression of nearby genes as a consequence of their insertion into or excision from plasmid genomes.

Restriction and modification in B. subtilis. Nucleotide sequence recognised by restriction endonuclease R. Bsu R from strain R

Restriction endonuclease R from Bacillus subtilis strain R cleaves nonmodified SPP 1 DNA in approximately 80, and lambda DNA in about 200 different sites. DNA digests with this endonuclease and with endonuclease Hae III from Haemophilus aegyptius show identical fragmentation patterns on gel electrophoresis, indicating that the two enzymes recognise the same nucleotide sequence. The polynucleotide kinase reaction was used in conjunction with two-dimensional ionophoretic nucleotide mapping methods to identify the 5'-nucleotide sequences at the sites of cleavage by the B. subtilis restriction endonuclease. The results show that the recognition sequence is (see article) where arrows indicate the points of strand scission. Each of the four possible nucleotides can occur in the positions flanking the recognition site.

Site specific recA--independent recombination between bacterial plasmids: involvement of palindromes at the recombinational loci

A recA-independent recombinational event is described which results in insertion of an entire plasmid genome at a unique site of another plasmid, and coincident excision of a precisely defined DNA segment originally present at the point of the insertion. The resulting recombinant molecules subsequently can undergo site-specific translocation of their component segments or inversion of their original DNA sequence orientation. The events observed entail nonreciprocal exchange of genetic material, and involve a discrete nucleotide sequences that is duplicated in rotationally symmetrical reverse orientation on plasmid DNA (i.e., inverted repeat; palindrome).

On the statistical significance of primary structural features found in DNA-protein interaction sites

Probabilities of occurrence for a number of the symmetries and other sequence regularities found in DNA-protein interaction site sequences have been calculated for segments of random DNA sequence. Results show that many of the symmetrical and repetitive features seen in these interaction sites are likely to have occured by chance. Other features are so unlikely to have occurred by chance that they are probably involved in the DNA-protein interaction processes.

The behaviour of oligodeoxynucleotides on thin-layer chromatography on polyethyleneimine-cellulose and ion-exchange paper electrophoresis. Applications in fractionating and sequencing terminally labelled oligodeoxynucleotides

The electrophoretic behaviour of oligodeoxynucleotides on ion-exchange papers was studied systematically with particular attention to applications in sequence analysis. Complex mixtures of larger oligonucleotides were fractionated by electrophoresis on cellulose acetate followed by t.l.c. on polyethyleneimine-cellulose. The behaviour of the oligonucleotides on polyethyleneimine-cellulose and on the two-dimensional system can provide a useful guide to their sequence. Detailed results from some of these experiments have been deposited as Supplementary Publication SUP 50031 (13 pages) at the British Library (Lending Division) (formerly the National Lending Library for Science and Technology), Boston Spa, Yorks. LS23 7BQ, U.K., from whom copies can be obtained on the terms indicated in Biochem. J. (1973), 131, 5.

DNA sequence analysis: a general, simple and rapid method for sequencing large oligodeoxyribonucleotide fragments by mapping

Several electrophoretic and chromatographic systems have been investigated and compared for sequence analysis of oligodeoxyribonucleotides. Three systems were found to be useful for the separation of a series of sequential degradation products resulting from a labeled oligonucleotide: (I) 2-D electrophoresisdagger; (II) 2-D PEI-cellulose; and (III) 2-D homochromatography. System (III) proved generally most informative regardless of base composition and sequence. Furthermore, only in this system will the omission of an oligonucleotide in a series of oligonucleotides be self-evident from the two-dimensional map. The sequence of up to fifteen nucleotides can be determined solely by the characteristic mobility shifts of its sequential degradation products distributed on the two-dimensional map. With this method, ten nucleotides from the double-stranded region adjacent to the left-hand 3'-terminus and seven from the right-hand 3'-terminus of bacteriophage lambda DNA have been sequenced. Similarly, nine nucleotides from the double-stranded region adjacent to the left-hand 3'-terminus and five nucleotides from the right-hand terminus of bacteriophage phi80 DNA have also been sequenced. The advantages and disadvantages of each separation system with respect to sequence analysis are discussed.

Alignment of two DNA helices: a model for recognition of DNA base sequences by the termini-generating enzymes of phage lambda, 186, and P2

Based on the 3'- and 5'-terminal sequences of DNA of phage lambda, P2, and 186, a model is proposed for recognition of DNA sequences by enzymes responsible for generation of cohesive ends. Two copies of the cohered ends, either on separate molecules or on a concatemer, are aligned with their helical axes parallel but running in opposite directions. The nicking system is dimeric, with each of the two monomers carrying identical sequence-recognition sites. Two pairs of nicks are introduced into the two aligned DNA molecules by the nicking system. The applicability of this model to other biological processes, such as integration of a viral genome into a host genome and the cutting of concatemeric T7 DNA, is discussed.