Transcription Factors in Fungi: TFome Dynamics, Three Major Families, and Dual-Specificity TFs

Frontiers in Genetics
Ekaterina Shelest

Abstract

Transcription factors (TFs) are essential regulators of gene expression in a cell; the entire repertoire of TFs (TFome) of a species reflects its regulatory potential and the evolutionary history of the regulatory mechanisms. In this work, I give an overview of fungal TFs, analyze TFome dynamics, and discuss TF families and types of particular interest. Whole-genome annotation of TFs in more than 200 fungal species revealed ~80 families of TFs that are typically found in fungi. Almost half of the considered genomes belonged to basidiomycetes and zygomycetes, which have been underrepresented in earlier annotations due to dearth of sequenced genomes. The TFomes were analyzed in terms of expansion strategies genome- and lineage-wise. Generally, TFomes are known to correlate with genome size; but what happens to particular families when a TFome is expanding? By dissecting TFomes into single families and estimating the impact of each of them, I show that in fungi the TFome increment is largely limited to three families (C6 Zn clusters, C2H2-like Zn fingers, and homeodomain-like). To see whether this is a fungal peculiarity or a ubiquitous eukaryotic feature, I also analyzed metazoan TFomes, where I observed a similar trend (limited ...Continue Reading

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Citations

Aug 30, 2019·The Journal of Microbiology·Min-Ju KimHee-Soo Park
Oct 4, 2018·Frontiers in Bioengineering and Biotechnology·Glaucia Emy Okida MidorikawaRobert Neil Gerard Miller
Jan 31, 2020·Frontiers in Microbiology·Alex Machio KangeDaolong Dou
May 12, 2021·Molecular Plant Pathology·Evan JohnKar-Chun Tan
Jun 8, 2021·Frontiers in Microbiology·Cinthia V Soberanes-GutiérrezEdgardo Galán-Vásquez

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Software Mentioned

InterProScan
MetaPhOrs
PhyML
Muscle
InterPro
Phylome DB Blast

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