Final answer:
The RNAP holoenzyme recognizes different gene promoters through the binding of alternative specialized sigma subunits, each of which recognizes specific cis-element sequences and configurations of the promoter. The correct option is C.
Step-by-step explanation:
The RNAP (RNA polymerase) holoenzyme recognizes different gene promoters primarily by binding alternative specialized sigma subunits. These sigma subunits effectively distinguish between various cis-element sequences and configurations of the promoter.
Each sigma subunit is specialized to recognize a specific set of promoter sequences, consistent with the bacterial operon model where the regulation of gene expression is directed by the interaction of various transcription factors, including sigma factors, with the promoter regions.
It's important to acknowledge that the process of transcription is highly complex and involves the DNA-binding proteins and regulatory sequences such as the TATA box, GC box, and enhancer regions. The specific interactions between these elements allow for the finely tuned regulation of gene expression necessary for cellular function and response to environmental changes.
Contrary to the options A, B, and D which involve more mechanical or localized structural changes of the RNA polymerase itself, it is the binding of different sigma subunits (option C) that primarily facilitates promoter recognition. This exemplifies the significance of protein-protein interactions over mere structural changes within RNAP, in promoter specificity.