Circular monomers of bacteriophage lambda DNA as substrates for in vitro packaging

In vivo packaging of bacteriophage lambda monomeric chromosomes

There is an apparent paradox between the reported requirements for lambda DNA packaging in vivo and in vitro. In vivo, DNA concatemers are required for packaging. On the other hand, in vitro, packaging extracts can encapsidate either linear or circular monomeric lambda DNA. Perhaps cellular nucleases restrict the in vivo ability of monomers to package by degrading a free double chain end present as an intermediate in the packaging reaction. Consistent with this hypothesis, enhanced packaging of monomers was found in an ExoV- host. No additional enhancement was noted in a host also mutant for sbcB and sbcC. We isolated a mutant phage for which in vivo packaging of monomeric lambda chromosomes is increased about 10(3)-fold. The responsible mutation (plm1 for packages lambda monomers) was mapped to cro, sequenced, and found to cause a change from Ala29 to Ser in the alpha3 helix of Cro's DNA binding domain. Density transfer experiments showed that packaging of both plm1 and wild-type lambda was aided by allowing some DNA synthesis. However, the packaged chromosomes had not themselves undergone a full round of replication and therefore were not part of a canonical concatemer made by replication. Other tests showed that packaged phage had not been part of concatemers made by recombination or by annealing at cos. Our results with wild-type lambda also favor models in which two cos sites are needed for packaging, but these sites need not be in cis. In lambda plm1, replication intermediates may serve as substrates for encapsidation.

A phosphate group at the cos ends of phage lambda DNA is not a prerequisite for in vitro packaging: an alternative method for constructing genomic libraries using a new phasmid vector, lambda pGY97

It is shown here that the phosphate groups at the cos ends of phage lambda DNA are not a prerequisite for in vitro packaging. Molecules with phosphatase-treated cos ends are packaged in vitro as efficiently as native lambda DNA. This observation can be used for an alternative strategy to improve the efficiency of gene library construction, since cos-cos ligation decreases in vitro encapsidation and infectivity. Dephosphorylated cos ends and a new phasmid vector lambda pGY97 have been used to construct a representative gene bank of alfalfa in a Mcr- (5-methylcytosine restriction deficient) Escherichia coli host strain. These recombinant clones can be propagated as phages or more conveniently as plasmids in recA- E. coli, to prevent possible homologous recombination events between repetitive sequences of the insert that would otherwise interfere with clone stability. The 5-19-kb inserts can be easily recloned as plasmids from the recombinant phasmids with simple EcoRI digestion and re-ligation. This observation also implies that the construction of gene libraries in cosmid vectors can be made more efficient if cos-cos ligates were cleaved by lambda terminase just before in vitro packaging.

A bacterial protein requirement for the bacteriophage lambda terminase reaction

The bacteriophage lambda terminase enzyme cleaves the cohesive-end sites of lambda DNA to yield the protruding 5'-termini of the mature molecule. In vitro, this endonucleolytic event requires a protein factor which has been isolated and purified from extracts of uninfected E. coli. The terminase host factor (THF) is a heat stable basic protein of M.W. approximately 22,000. The integration host factor (IHF) protein of E. coli can efficiently substitute for THF in the terminase reaction; however, THF can be demonstrated to be physically present in, and isolated with full biological activity from extracts of cells defective or deficient in IHF.

Improved in vitro packaging of coliphage lambda DNA: a one-strain system free from endogenous phage

In previous systems for in vitro packaging of lambda DNA, phages are produced from the packaging components as well as from added DNA. We have developed a new genetic strategy for in vitro packaging that bypasses this endogenous phage problem. Our system employs a single bacterial strain whose lambda prophage codes for all of the packaging proteins but is deleted for cos, the packaging origin. Crude extracts of the single lysogen: (i) are virtually free from endogenous phages, (ii) package added lambda DNA efficiently and (iii) are easy to prepare. Using the cos- in vitro packaging system we show that packaging of lambda linear monomers is a second-order reaction, but that packaging from concatemers prepared by annealing or ligation is first order. We conclude that in our cos- system, linear monomers are a poor substrate for in vitro packaging but that packaging from concatemers works well.

The maturation of coliphage lambda DNA in the absence of its packaging

In vivo, lambda DNA cannot be cleaved at cos (matured) if proheads are not present; in vitro, however, cos cleavage readily takes place in the absence of proheads. In order to investigate this paradox, we have constructed plasmids that synthesize lambda terminase in vivo upon induction. The plasmids also contain cos at the normal position, about 190 bp upstream of lambda gene Nul. One of the plasmids, pFM3, produces levels of terminase comparable to those found after phage induction. If cells carrying pFM3 are thermoinduced, almost 100% of the intracellular plasmid DNA has a double-strand interruption at or near cos. Since the only lambda genes that pFM3 carries are Nul, A, W and B, this in vivo cleavage is occurring in the absence of proheads. Previous failure to observe lambda maturation with phages carrying prohead mutations may be due to exonucleolytic degradation of the unprotected DNA ends, a different DNA topology or compartmentalization, or terminase inhibition in the absence of prohead by the product of another lambda gene that maps to the right of gene B.