The Evolving Story of Phage λ Transcriptional Control: Enhancer-like Transcriptional Activation by the OL Operator

Article: Cui, L., Murchland, I., Shearwin, K.E., Dodd, I.B. (2013)  Enhancer-like long-range transcriptional activation by λ CI-mediated DNA looping.  PNAS 110(8):2922-2927.

At the level of gene regulation, phage λ is probably the best-understood organism on Earth.  Yet, every time I think we have most of this phage figured out and there is not much else to learn, I read yet another interesting and insightful article about λ.

For those who are not familiar with phage λ genetic circuitry or don’t remember it from genetics class, here is a primer on the basics: The genetic switch controls whether an infecting phage undergoes lytic or lysogenic growth and in phage λ this is centrally controlled by whether or not the cI repressor gene is expressed.  The default decision is to undergo lytic growth whereby the phage replicates within the host cell and lyses the cell, releasing progeny, unless repressor is made.  CI is expressed from the P_RM promoter and there is a divergent, lytic promoter, P_R, which drives expression of cro. Cro antagonizes CI and drives lytic growth.  These two promoters are both controlled by the operator O_R, which is actually three operator sites (O_R1, O_R2, O_R3).  CI binds cooperatively to O_R1 and O_R2, shutting down expression from PR and thus lytic growth.  It also activates its own expression at P_RM.  When concentrations of CI in the cell are sufficient it binds to O_R3 and blocks its own transcription, thus maintaining a steady state of CI in the cell.  Not only does CI bind to the O_R sites cooperatively, but there are similar sites ~2.3 Kbp away at the O_L operator that also binds CI.  Further cooperativity between CI bound at O_R and O_L leads to DNA looping, further enhancing the activation and repression of the P_RM and P_R promoters, respectively.  (If this is a bit much, there is a great minireview on λ genetics by Court, Oppenheim and Adhya¹ that gives a more in depth explaination)

How DNA looping enhances repression of P_R is pretty straight forward, but what has not been well understood is how the O_L site increases CI activation of P_RM.   Cui et al. provide support for the “UP contact model” in which O_L-O_R looping brings an UP element for the P_L promoter close enough to P_RM so that it can be contacted by the C-terminal domain of the α-subunit of an RNA polymerase bound at P_RM.  They show that activation requires the UP element, an intact α C-terminal domain and CI-mediated DNA looping, thus confirming the model.  Furthermore, they provide structural models supporting the feasibility of contact between the UP element and the α-subunit.  The figure above (Fig. 4D in the article) shows an octamer of CI bound at two O_R and two O_L sites looping the DNA so that the α-subunit (green) of RNA polymerase (yellow) can contact the UP element (blue).

Enhancer elements are quite intriguing genetic elements that can activate transcription at a promoter located several kilobases away.  They are widespread, existing in eukaryotes, prokaryotes and phage, yet our understanding of how enhancer-promoter complexes work at a mechanistic level still lacks many details.  Cui et al. have uncovered an enhancer-like element in λ that both provides further insight into λ genetic circuitry and a potential model for enhancer elements.  What wonders will be revealed about this 48.5 Kbp piece of DNA we call λ in the near future?  I can’t wait to find out!

1. Court, D., et al. 2007. A new look at bacteriophage λ genetic networks. 189(2): 298-304.