Sequence Tolerance of the Phage λ P RM Promoter: Implications for Evolution of Gene Regulatory Circuitry
Open Access
- 1 December 2004
- journal article
- research article
- Published by American Society for Microbiology in Journal of Bacteriology
- Vol. 186 (23), 7988-7999
- https://doi.org/10.1128/jb.186.23.7988-7999.2004
Abstract
Much of the gene regulatory circuitry of phage λ centers on a complex region called the O R region. This ∼100-bp region is densely packed with regulatory sites, including two promoters and three repressor-binding sites. The dense packing of this region is likely to impose severe constraints on its ability to change during evolution, raising the question of how the specific arrangement of sites and their exact sequences could evolve to their present form. Here we ask whether the sequence of a cis -acting site can be widely varied while retaining its function; if it can, evolution could proceed by a larger number of paths. To help address this question, we developed aλ cloning vector that allowed us to clone fragments spanning the O R region. By using this vector, we carried out intensive mutagenesis of the P RM promoter, which drives expression of CI repressor and is activated by CI itself. We made a pool of fragments in which 8 of the 12 positions in the− 35 and −10 regions were randomized and cloned this pool into the vector, making a pool of P RM variant phage. About 10% of the P RM variants were able to lysogenize, suggesting that the λ regulatory circuitry is compatible with a wide range of P RM sequences. Analysis of several of these phages indicated a range of behaviors in prophage induction. Several isolates had induction properties similar to those of the wild type, and their promoters resembled the wild type in their responses to CI. We term this property of different sequences allowing roughly equivalent function “sequence tolerance ” and discuss its role in the evolution of gene regulatory circuitry.Keywords
This publication has 50 references indexed in Scilit:
- Subunit Structure of Regulator Proteins Influences the Design of Gene Circuitry: Analysis of Perfectly Coupled and Completely Uncoupled CircuitsJournal of Molecular Biology, 1995
- Direct and Indirect Effects of Mutations in λ PRM on Open Complex Formation at the Divergent PR PromoterJournal of Molecular Biology, 1994
- λ Repressor mutants that are better substrates for RecA-mediated cleavageJournal of Molecular Biology, 1989
- Interactions between Escherichia coli RNA polymerase and lambda represser mutations in PRM affect repression of PRJournal of Molecular Biology, 1988
- Kinetics of open complex formation between Escherichia coli RNA polymerase and the lac UV5 promoter. Evidence for a sequential mechanism involving three stepsBiochemistry, 1985
- A pSC101-derived plasmid which shows no sequence homology to other commonly used cloning vectorsGene, 1984
- Repressor cleavage as a prophage induction mechanism: Hypersensitivity of a mutant λ cI protein to RecA-mediated proteolysisJournal of Molecular Biology, 1981
- Gene regulation at the right operator (OR) of bacteriophage λJournal of Molecular Biology, 1980
- Gene regulation at the right operator (OR) of bacteriophage λJournal of Molecular Biology, 1980
- DNA sequence of the bacteriophage λ cI geneNature, 1978