iTAK: A Program for Genome-wide Prediction and Classification of Plant Transcription Factors, Transcriptional Regulators, and Protein Kinases

Abstract

Transcription factors (TFs) are proteins that regulate the expression of target genes by binding to specific cis-elements in promoter regions. Transcriptional regulators (TRs) also regulate the expression of target genes; however, they operate indirectly via interaction with the basal transcription apparatus (e.g. TFs), or by altering the accessibility of DNA to TFs via chromatin remodeling. Another type of regulatory proteins, protein kinases (PKs), function in signal transduction pathways and alter the activity of target proteins by phosphorylating them. These three important classes of regulatory proteins have been associated with numerous aspects of plant growth and development (Gapper et al., 2014; Xu and Zhang, 2015), and response to biotic and abiotic stimuli (Mickelbart et al., 2015; Zhang et al., 2013). Effective and accurate identification and classification of these genes is important for understanding their evolution, biological functions, and regulatory networks. Currently, more than 100 plant genomes have been sequenced and regulatory proteins have been systematically identified from several of these plant genomes. Databases presenting these regulatory proteins, especially TFs, have been developed, such as PlnTFDB (Pérez-Rodríguez et al., 2010) and PlantTFDB (Jin et al., 2013). However, annotations of TF/TR families and the associated classification rules have been inconsistent among different studies. For example, the PlantTFDB does not include TRs that are presented in PlnTFDB. As another example, the ?forbidden? domain (a domain that the specific TF families should not contain) of the C2H2 family is annotated as an RNase_T domain in PlantTFDB, but as a PHD domain in PlnTFDB. Presently, while the collection of genome sequences is rapidly expanding, cataloged and annotated TFs/TRs vary across different databases due to inconsistent identification and characterization criteria with serious consequences for genome scale and targeted analyses. Furthermore, in contrast to many studies focusing on specific families of plant regulators, computational tools for identification and classification of these regulatory proteins on a genome scale are very limited.