bindigenes

Bindigenes are a proposed class of genes that encode proteins specialized in mediating binding interactions within the cell. The products of bindigenes can interact with ligands, nucleic acids, other proteins, or membranes, and through these interactions they influence the formation, stability, and activity of macromolecular complexes. The concept is used in theoretical and synthetic biology discussions to describe how genetic information can shape cellular networks by modulating binding events rather than solely altering catalytic activity.

Most bindigenes are envisioned as encoding modular proteins with one or more binding domains. Domain types commonly cited include DNA-binding motifs, protein-protein interaction modules, RNA-binding regions, and small-molecule or lipid-binding pockets. The arrangement and combination of domains determine binding specificity and allow the construction of diverse interaction networks. In many models, binding states respond to environmental cues or developmental signals by changing affinity or conformational state, thereby routing cellular programs.

In natural systems, bindigenes are thought to influence signaling pathways, gene regulation, transport, and metabolic flux by governing when and where molecular complexes form. They can affect localization, assembly of multiprotein machines, and cross-talk between pathways, contributing to processes such as development, immunity, and stress responses.

Evolutionary considerations suggest bindigenes are widespread but vary in specialization. Gene duplication, domain shuffling, and regulatory rewiring can expand or modify binding repertoires across lineages.

Methods to study bindigenes include binding assays, structural biology, interactome mapping, and computational predictions, complemented by genetic perturbations. Challenges include binding promiscuity, context dependence, and functional redundancy.

Some researchers view bindigenes as a useful unifying concept for understanding how binding interactions shape cellular programs, while others regard the term as overlapping with established categories such as transcription factors or binding receptors.