Regulation of repressor and early gene expression in Mu-like transposable bacteriophage D108

The temperate, transposable bacteriophages D108 and Mu are highly homologous, but differ in their lef-end regulatory regions. We have previously cloned the gene encoding the D108 thermo-sensitive (cts) repressor under the control of the lactUV5 promoter. In this work, we report that crude protein extracts containing highly-expressed D108 repressor protect a 77 bp region of DNA, located between 863 bp and 940 bp from the D108 lef--end, from both exonuclease III and DNase I hydrolysis. Nucleotide sequence analysis of this region reveals that is also contains DNA sequences homologous to the consensus DNA-binding site of the Escherichia coli protein, Integration Host Factor (IHF). Crude protein extracts containing highly-expressed IHF specifically bind to, and retard the migration of, DNA fragments containing the D108 regulatory region, and the DNA sequence which IHF protects from DNase I cleave lies directly within the D108 repressor binding region. There are two apparent repressor-specific S1 nuclease-resistant RNA suggests that transcription from the early region promoter, Pe may initiate at or about 1000 bp from the left-end of the D108 genome. Thus though, D108 and Mu utilize three analogous proteins (repressor, ner, and IHF) and the same apparent promoters for early gene regulation and the lytic/lysogenic decision, the organization of these regulatory components is apparently different, suggesting different mechanisms of control of gene expression.