Table 1. Definition of key terms and abbreviations.

Term or abbreviation	Definition
Fitness	We define fitness as the success of an organism in a given environment. Success is determined as growth rate in pure cultures or abundance in competition cultures
Regulatory program	A ‘regulatory program’ or ‘program’ is defined as a set of instructions for the differential regulation of a group of genes. A TFB program then refers to a set of instructions specified by that TFB. A program is encoded in the regulation of a TFB and its interactions (protein–protein–DNA) with other genes (including other transcription factors and regulators)
Niche adaptation program	A program that is essential for adaptation to a particular environment or niche
Reprogramming	Reprogramming refers to changes in either the regulation of a TFB or its interactions that result in changes to differential regulation of genes
Relative importance of a TFB	Percent contribution of a TFB toward fitness in a particular environment
GRN	Gene regulatory network
GTF	General transcription factor
TF	Transcription factor
TFB	Transcription factor B
TBP	TATA-binding protein