Deletion, recombination and gene expression involving the bacteriophage lambda attachment site

Yeast HIS3 expression in Escherichia coli depends upon fortuitous homology between eukaryotic and prokaryotic promoter elements

The yeast imidazoleglycerolphosphate dehydratase gene HIS3, when introduced into Escherichia coli, is transcribed and translated with sufficient fidelity to produce functional enzyme. The following lines of evidence indicate that E. coli RNA polymerase recognizes a particular region of HIS3 DNA as a promoter sequence. First, this promoter contains nucleotide sequences that resemble the canonical prokaryotic promoter elements, the -10 and -35 regions. Second, HIS3 transcription in vitro by E. coli RNA polymerase is initiated at the predicted site downstream from the conserved sequences. Third, deletion mutations that successively encroach upon the 5' end of the HIS3 gene indicate that the promoter is necessary and sufficient for expression in E. coli. Fourth, a single base-pair change that behaves as an "up-promoter" mutation alters the -35 region such that it becomes identical with the consensus sequence. Because the -10 region of this promoter coincides with the TATA promoter element that is necessary for expression in yeast cells, it is possible directly to compare prokaryotic and eukaryotic promoter function. Analysis of 51 deletion and substitution mutations indicates that the patterns of mutant phenotypes are quite different for each organism. Therefore, although prokaryotic -10 regions are similar in sequence to eukaryotic TATA elements and although the same his3 region serves both functions, it appears that this represents an evolutionary coincidence whose current functional basis is minimal. The evolutionary significance of the homology between prokaryotic and eukaryotic promoter elements is discussed.

Patterns of lambda Int recognition in the regions of strand exchange

Int protein has two classes of binding sites within the phage att site: the arm-type recognition sequences are found in three specific sites that are distant from the region of strand exchange; the junction-type recognition sequences occur as inverted pairs around the crossover region in both attP and attB. During recombination between attP and attB each of the four DNA strands is cut at a homologous position within each of the junction-type Int binding sites. In all four junction-type sites Int protein interacts primarily with the same face of the DNA helix, as determined by those purine nitrogens that are protected against methylation by dimethylsulfate. Efficient secondary attachment sites for lambda contain sequences with partial homology to the junction-type binding sites. In addition, the sequence between, but not part of, the two junction-type sites (the overlap region) is strongly conserved in secondary att sites. Thus, in the vicinity of strand exchange, attP and a recombining partner, such as attB, are very similar; each comprises two junction-type Int recognition sites and an overlap (crossover) region.