An Ode to λ

 

I grew up in the phage group and spent many summers at the phage meetings in Cold Spring Harbor. Back then (late 1960s, early 1970s), the best scientists worked on bacteriophage λ (lambda) and the rest of us just tried to keep up.

A number of key insights in molecular biology came from studying this small virus that infects Escherichia coli and if you didn't know about that research you were really out of the loop.

But by 1990 it was already apparent that a new generation of students was growing up in ignorance of the fundamental concepts learned from studying bacteriophage and bacteria. I remember asking a class what they knew about the genetic switch in bacteriophage λ and getting nothing but blank looks! Everyone worked on eukaryotes by then and the knowledge acquired by the phage group was not relevant.

I tried to teach that knowledge in my classes. In my textbook I devoted 27 pages to describing the regulation of phage genes (in a chapter on "Gene Expression and Development"). Other instructors didn't care.

Here's a short list of things we learned from studying λ. How many have you learned?

1. Mutants in the E gene of λ can be rescued by an important class of bacterial mutations in two different genes: groE and groL. What do the products of those genes do?
2. The integration of λ DNA into the bacterial genome to form a prophage occurs at a single specific site in the bacterial chromosome. How does this classic example of site specific recombination work?
3. The λ genome is a linear molecule 49kb in length. All of it is replicated accurately, including the ends. How does this work?
4. The phage has dozens of genes but only two of them are transcribed immediately after infection (immediate early genes: N and cro). Why aren't the others transcribed?
5. The product of gene N is an antiterminator and it's expression allows transcription of several early genes (cro, cII, O, P, Q, cIII, Xis, and Int). How does antitermination work and what did we learn about transcription complexes and the importance of NusA?
6. Very early in a lytic infection there is a small RNA (6S RNA) produced in huge amounts from the P_R' promoter. The RNA does not encode any protein and has no function. Why is it produced?
7. cII is a well-studied example of a transcriptional activator that recognizes multiple promoters. How does it work?
8. The λ repressor (cI) is both a repressor and an activator. So is cII. We now know that many transcriptional regulators function as both repressors and activators. What is the mechanism?
9. Two transcriptional regulators, cI and cro, bind to the same six operators but have opposite effects. We now know of many examples of this kind of competition. How does it work?

10. When sufficient copies of lambda repressor (cI) are made, transcription of all early and late genes is repressed. Why doesn't this happen during a normal lytic infection?
11. In order to induce the prophage, the repression by cI has to be blocked. What circumstances cause this and what is the mechanism?
12. The expression of the Q gene is inhibited by an antisense RNA. How does antisense RNA regulate gene expression?
13. The structures of cI and cro revealed a universal DNA binding domain found in many transcriptional regulators, including the HOX proteins. What is that domain and how does it interact with DNA?
14. One of the strong leftward promoters, P_INT, is right in the middle of the xis gene and this is related to control of integrase synthesis by regulating the stability of its mRNA. How?
15. The genetic switch is an excellent and very well understood example of developmental regulation of gene expression. Do you know how it works?
16. Bacteriophage λ infection is enhanced by maltose. This led to an understanding of cell surface receptors. How?

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[Image Credit: The bottom two figures are from Microbiology 2nd ed. by J.L. Slonczewski and J.W. Foster, W.W. Norton & Co. Inc., 2010]