Controller node complexity: A measure of the degree of gene coordination

Summary

For the comparative study of gene regulation, the concept of a controller node is made use of. A controller node is the set of molecular components directly intervening in the control of RNA derived from a functional unit of gene action (abbreviated fuga). The complexity of a controller node is defined here as the number per fuga of distinct components included in the controller node relevant to a given fuga. Two types of controller node are distinguished: transcriptional and processing. The complexity of a transcriptional controller node is the sum of distinct receptor sequences in the fuga, distinct regulator molecules that interact with them, and distinct effector molecules or modifying enzymes that interact with the regulator molecules. Likewise, processing controller node complexity is the sum of distinct receptor sequences on an intact nuclear RNA transcript, distinct processor molecules that interact with the receptors, and distinct effector molecules or modifying enzymes that interact with the processors. For valid comparisons between widely different organisms, values for transcriptional and processing controller node complexity might in the future be combined to yield a value for conjugate controller node complexity. Some conventions for evaluating controller node complexity are proposed and are applied to a few bacterial operons. Particular conditions of the application of the concept to eukaryote fugas are discussed. Average controller node complexity per organism or per genetic subsystem is a measure of the amount of gene coordination. This value would also reflect the hierarchical complexity of organisms, if it increased during progressive evolution.