The role of the direct repeat in qut-controlled antitermination in phage lambda

For antitermination of transcription from the late p'R promoter of phage lambda, a cis-acting qut sequence, which overlaps with p'R, is required, together with the product of lambda gene Q. Using our BspMI-mediated multicycle technique for generation of precise deletions, we have confirmed that deletions removing DNA downstream of +18 bp (counted from the p'R-controlled transcriptional start point s'R = +1) do not affect the efficiency of qut antitermination; at the same time we found that deleting one more bp (shifting the right-hand boundary to bp +17) reduces antitermination by only 20%. Deleting another 5 or 6 bp (+11 or +12 bp right-hand qut boundary), decreases antitermination by about 80%. These deletions reduce the 9/10-bp-direct repeat (5'-TGGGT(A or T)AATT)2 in qut to only the five italicized bp. Similar strong reduction in antitermination (by about 68%) was obtained with +16 bp qut boundaries, in constructs which also contained 2- or 3-bp insertions between bp +11 and +12 or between +12 and +13. Since the latter deletions retain only 5/10 bp of the direct repeat, it appears that antitermination is dependent on the length and intactness of the direct repeat.