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. GRNs are rewired through events including the duplication of TF-coding genes, their divergent sequence evolution and the gain/loss/modification of CRSs. Fungi (mainly Saccharomycotina) have served as a reference kingdom for the study of GRN evolution. Here, I studied the genes predicted to encode TFs in the fungus Aspergillus nidulans (Pezizomycotina). The analysis of the expansion of different families of TFs suggests that the duplication of TFs impacts the species level, and that the expansion in Zn2Cys6 TFs is mainly due to dispersed duplication events. Comparison of genomic annotation and transcriptomic data suggest that a significant percentage of genes should be re-annotated, while many others remain silent. Finally, a new regulator of growth and development is identified and characterized. Overall, this study establishes a novel theoretical framework in synthetic biology, as the overexpression of silent TF forms would provide additional tools to assess how GRNs are rewired.
Highlights
The Set of Potential transcription factors (TFs) in the Ascomycete Fungus Aspergillus nidulans Is Dominated by Binuclear Zinc Clusters
TFs and Gene regulatory networks (GRNs) controlling in fungi, e.g., stress-response, carbon and nitrogen metabolism, light sensing and the induction/progression of developmental cycles were characterized for the first time in this Aspergillus species
To explore new features of its TFome, the conservation and expression patterns of the genes encoding these TFs, and uncover new traits of the organization and evolution of GRNs in the kingdom fungi, firstly, I updated the list of TFs potentially encoded in the genome of A. nidulans
Summary
Transcription factors (hereafter referred to as TFs) are proteins that are capable of binding DNA at cis-regulatory sequences (CRSs) of target genes. TF-CRS binding repress or promote transcription by RNA polymerase. The biological impact of most TFs cannot be completely assessed individually but collectively, as interacting units of a network or interconnected networks of TFs, associated proteins and CRSs, which are generally known as gene regulatory networks or GRNs [1]. The architecture of GRNs ranges from simple, such as that controlling mating-type in yeasts [2], to complex, multistep hierarchical and democratic relationships formed by multiple TFs and associated proteins, such as the biofilm network of Candida albicans or the embryonic stem cell network of Mus musculus (compared by [3])
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