Transcription factors in the fungus Aspergillus nidulans: Markers of genetic innovation, network rewiring and conflict between genomics and transcriptomics

Abstract

Gene Regulatory Networks (GRNs) are shaped by the democratic/hierarchical relationships among transcription factors (TFs) and associated proteins, together with the cis-regulatory sequences (CRSs) bound by these TFs at target promoters. GRNs control all cellular processes, including metabolism, stress-response, growth and development. Due to the ability to modify morphogenetic and developmental patterns, there is the consensus view that the reorganization of GRNs is a driving force of species evolution and differentiation. Duplication of genes coding for TFs, their divergent sequence evolution and gain/loss/modification of CRSs are events causing GRN rewiring. Fungi (mainly Saccharomycotina) have served as a reference kingdom for the study of GRN evolution. Here, I studied the genes predictably coding for TFs in the fungus Aspergillus nidulans (Pezizomycotina). Bioinformatics results support the view that duplication events of TF-coding genes potentially impact the species levels. Discrepancy between gene-annotation and transcriptomic data suggests that duplication of genes potentially coding for TFs are not always accompanied by the generation of functional forms and modification of regulatory potential. Overall, this study establishes a novel theoretical framework in synthetic biology, since overexpression of silent or primarily non-functional TF forms would provide additional tools for assessment of the mechanisms triggering GRN rewiring.