A genetic network that balances two outcomes utilizes asymmetric recognition of operator sites

Research on phage λ: a lucky choice

Bacteriophage λ is a paradigm in the field of gene regulation and one of the best-understood systems in genetic regulatory biology. A so-called Genetic Switch determines the mechanisms by which λ transitions to its dual lifestyles-lytic or lysogenic. When λ initiates the lysogenic lifestyle, the phage-encoded CI repressor binds cooperatively to multi-partite operators in a defined pattern that autoregulates repression of phage lytic promoters as well as activation of the lysogenic promoter. The study of this genetic switch and related earlier research on phage λ revealed the main principles of gene expression and regulation in molecular biology. This article describes the underlying molecular details of λ lysogeny, as it is currently understood.

Specific DNA sequences allosterically enhance protein-protein interaction in a transcription factor through modulation of protein dynamics: implications for specificity of gene regulation

Most genes are regulated by multiple transcription factors, often assembling into multi-protein complexes in the gene regulatory region. Understanding of the molecular origin of specificity of gene regulatory complex formation in the context of the whole genome is currently inadequate. A phage transcription factor λ-CI forms repressive multi-protein complexes by binding to multiple binding sites in the genome to regulate the lifecycle of the phage. The protein-protein interaction between two DNA-bound λ-CI molecules is stronger when they are bound to the correct pair of binding sites, suggesting allosteric transmission of recognition of correct DNA sequences to the protein-protein interaction interface. Exploration of conformation and dynamics by time-resolved fluorescence anisotropy decay and molecular dynamics suggests a change in protein dynamics to be a crucial factor in mediating allostery. A lattice-based model suggests that DNA-sequence induced allosteric effects could be crucial underlying factors in differentially stabilizing the correct site-specific gene regulatory complexes. We conclude that transcription factors have evolved multiple mechanisms to augment the specificity of DNA-protein interactions in order to achieve an extraordinarily high degree of spatial and temporal specificities of gene regulatory complexes, and DNA-sequence induced allostery plays an important role in the formation of sequence-specific gene regulatory complexes.