Modifying native organism through evolutionary engineering for desirable purpose often provides great breakthroughs to challenging obstacles in areas within biotechnology including biofuel production, screening of desirable phenotypes, etc. Conventional mutation methods, however, can be biased to certain types of mutations which restrict the accessibility to desirable phenotypes. In this study, we evaluated the potential of the library of synthetic zinc linger protein transcription factors (synthetic ZFP-TF library) for overcoming such limits. In the Saccharomyces cerevisiae sec14(ts) mutant background as a model eukaryotic system, we screened several sec14 bypass strains which can suppress growth defects through a malfunction of Sec14p with an introduced synthetic ZFP-TF library. Transcriptome analysis showed that many isolated strains exhibit simultaneous repression of genes which can suppress the growth defect. We also found that one of the isolated strains showed up-regulation of NTE1, which was not accessible by traditional evolutionary methods. These results showed that the synthetic ZFP-TF can affect multiple genes simultaneously and enables the activation of gene. Therefore, the synthetic ZFP-TF library can be a valuable tool to introduce global perturbations for phenotypic improvements and searching for unexplored phenotypic space to discover novel desirable phenotypes. (C) 2012 Elsevier Ltd. All rights reserved.