ABSTRACT
Lambdoid bacteriophage Q proteins are transcription antipausing and antitermination factors that enable RNA polymerase (RNAP) to read through pause and termination sites. Q proteins load onto RNAP engaged in promoter-proximal pausing at a Q binding element (QBE) and adjacent sigma-dependent pause element to yield a Q-loading complex, and translocate with RNAP as a pausing-deficient, termination-deficient Q-loaded complex. In previous work, we showed that the Q protein from bacteriophage 21 (Q21) functions by forming a “nozzle” that narrows and extends the RNAP RNA-exit channel, preventing formation of pause and termination RNA hairpins. Here, we report atomic structures of four states on the pathway of antitermination by the Q protein from bacteriophage λ (Qλ), a Q protein that shows no sequence similarity to Q21 and that, unlike Q21, requires the transcription elongation factor NusA for efficient antipausing and antitermination. We report structures of Qλ, the Qλ-QBE complex, the NusA-free “pre-engaged” Qλ-loading complex, and the NusA-containing “engaged” Qλ-loading complex. The results show that Qλ, like Q21, forms a nozzle that narrows and extends the RNAP RNA-exit channel, preventing formation of RNA hairpins. However, the results show that Qλ has no three-dimensional structural similarity to Q21, employs a different mechanism of QBE recognition than Q21, and employs a more complex process for loading onto RNAP than Q21, involving recruitment of Qλ to form a “pre-engaged” loading complex, followed by NusA-facilitated refolding of Qλ to form an “engaged” loading complex. The results establish Qλ and Q21 are not structural homologs and are solely functional analogs.
SIGNIFICANCE STATEMENT Bacteriophage Q proteins are textbook examples of regulators of gene expression that function at the level of transcription antitermination. Here, we report structures defining the mechanism of antitermination by the Q protein of bacteriophage λ (Qλ). The results show Qλ forms a “nozzle” that narrows and extends the RNA polymerase RNA-exit channel, precluding the formation of terminator RNA hairpins. The results show Qλ exhibits no structural similarity to the Q protein of bacteriophage 21 (Q21), employs a different mechanism for DNA binding than Q21, and employs a more complex process of loading onto RNA polymerase than Q21. We conclude Qλ and Q21 are not structural homologs and are solely functional analogs, akin to a bird wing and a bat wing.
Competing Interest Statement
The authors have declared no competing interest.
