Transcriptional antitermination activity of the synthetic nut elements of coliphage lambda. I. Assembly of the nutR recognition site from boxA and nut core elements

Phage λ--new insights into regulatory circuits

Bacteriophage λ, rediscovered in the early 1950s, has served as a model in molecular biology studies for decades. Although currently more complex organisms and more complicated biological systems can be studied, this phage is still an excellent model to investigate principles of biological processes occurring at the molecular level. In fact, very few other biological models provide possibilities to examine regulations of biological mechanisms as detailed as performed with λ. In this chapter, recent advances in our understanding of mechanisms of bacteriophage λ development are summarized and discussed. Particularly, studies on (i) phage DNA injection, (ii) molecular bases of the lysis-versus-lysogenization decision and the lysogenization process itself, (iii) prophage maintenance and induction, (iv), λ DNA replication, (v) phage-encoded recombination systems, (vi) transcription antitermination, (vii) formation of the virion structure, and (viii) lysis of the host cell, as published during several past years, will be presented.

The functional boundaries of the Q-utilization site required for antitermination of late transcription in bacteriophage lambda

Expression of the late genes of bacteriophage lambda requires, in addition to the host functions, the lambda p'R promoter, the antiterminator sequence qut, and the product of gene Q which interacts with the Q utilization (qut) site. In the absence of the Q function or qut site, the p'R-initiated transcription is blocked by the t'R terminator at the 194th nucleotide downstream of the start point, s'R, producing a short 6 S mRNA. In this study the position and boundaries of the qut site were deduced by constructing plasmids containing various portions of the p'R-qut region, the t'R1 terminator, and the reporter gene galK. We measured galK gene expression in response to the gamma Q gene product supplied in trans by a prophage or Q-expression plasmid. We show that among the lambda proteins, the Q gene product alone is necessary and sufficient for complete qut-mediated transcription antitermination in vivo. These antitermination experiments, employing plasmids that contain different lengths of lambda p'R-qut sequence, identified the right boundary of the qut site, which is located between +4 and +18 (for s'R = +1). The functional left boundary of qut does not extend upstream from the -26th nucleotide of the p'R promoter, as based on the following experiments. The promoter function of the truncated (-26)p'R-s'R-(+18) sequence can be restored by fusion to the complete but qut-less p'R, pp, or PLac promoter; however, no antitermination was observed for such a p-(-26)p'R-s'R-(+18)-t'R-galK plasmid. Thus we conclude that the qut site partially overlaps with the p'R promoter sequence. However, promoters that contain the -10 region of p'R, s'R, and the +1 to +18 qut sequence did mediate Q-dependent antitermination when properly fused to the homologous or heterologous -35 promoter regions. Only those transcripts that start at s'R (+1 or very near to it) and also contain at least the first 18 nucleotides (actually greater than 4 and less than or equal to 18) of 6 S RNA appear to be a target for the Q-qut-mediated transcription antitermination, which acts not only at t'R but also at other Rho-independent or Rho-dependent terminators.

Effect of the promoter structure on the nutL transcription antitermination function

Several boxA-less 74-bp nutL antiterminator fragments do not function as antiterminators of plac-promoted transcription, but are active with the pp and p'R promoters at 30 degrees C. At elevated temperatures (42 degrees C), these defective 74-bp nutL modules retain 50% of their activity when controlled by the p'R promoter; with the pp promoter the antitermination activity is 5-10 times less efficient. Similarly, deletions of 1-3 bp in the spacer region between the boxA and boxB subunits of nutL (which abolish antitermination promoted by plac), allow rather efficient but thermosensitive antitermination when controlled by the pp or p'R promoter. These results point to possible conditional interactions between the promoter and antiterminator elements and functions. Also noted were unexpectedly slow mobilities of the p'R-nutL-bearing fragments, suggesting some unusual secondary structures.

Boundaries of the nutL antiterminator of coliphage lambda and effects of mutations in the spacer region between boxA and boxB

To study the relationship of sequence to function for the phage lambda nutL transcriptional antiterminator, we cloned the 354-bp HincII lambda DNA fragment (coordinates 35261-35615; Daniels et al., in Lambda II, 1983, pp. 485-486 and 618-619) between the plac promoter and Rho-dependent or Rho-independent terminators (t) in the plac-t-galK plasmid derived from vector pKO3, and assayed the galK expression in Escherichia coli hosts in the presence or absence of the N gene product. The 354-bp fragment displayed the complete antitermination activity, as did several shorter fragments obtained by restriction cutting, exonucleolytic deletions and ligations. The minimal length of cloned and fully active nutL comprises 43 bp and consists (in the 5'-to-3' order) of a 10-bp sequence upstream from boxA, the 8-bp boxA (5'-CGCTCTTA-3'), the 7-bp A-B spacer between boxA and boxB; the 17-bp boxB (nutL core; 5'-AGCCCTGAAGAAGGGCA-3') and 1-bp downstream from the nutL core. Deletion of the 10-bp sequence upstream from boxA reduces anti-termination by 40%. Deletion of both that sequence and boxA reduces antitermination by 90% at both 30 degrees C and 42 degrees C. Most of the deletions entering boxB abolish antitermination. Also, some of the small internal deletions within the 7-bp A-B spacer region have a strong negative effect on the nutL function, when transcription is from the plac promoter.