It is now generally accepted that most cellular phenotypes are affected by many genes. As a result, engineering a desired phenotype would be facilitated enormously by simultaneous multiple gene modification, yet the capacity to introduce such modifications is very limited. Here, we demonstrate that the components of global cellular transcription machinery (specifically, sigma(70)) can be engineered to allow for global perturbations of the transcriptome, which can help unlock complex phenotypes. Results from three distinct phenotypes (ethanol tolerance, metabolite overproduction, and multiple phenotypes) are provided as proof-of-concept. In each case, the tool of global transcription machinery engineering (gTME) outperformed traditional approaches by quickly and more effectively optimizing phenotypes.