iTAK: a program for genome-wide prediction and classification of plant transcription factors, transcriptional regulators, and protein kinases

ZHEN, YI; JIAO, CHEN; SUN, HONGHE; ROSLI, HERNÁN GUILLERMO; POMBO, MARINA ALEJANDRA; ZHANG, PEIFEN; BANF, MICHAEL; DAI, XINBIN; MARTIN, GREGORY; GIOVANNONI, JAMES; ZHAO, PATRICK X.; RHEE, SEUNG Y.; FEI, ZHANGJUN

MOLECULAR PLANT

OXFORD UNIV PRESS

Lugar: Oxford; Año: 2016

1674-2052

Transcription factors (TFs) are proteins that regulate the expression of target genes by binding tospecific cis-elements in promoter regions. Transcriptional regulators (TRs) also regulate theexpression of target genes; however, they operate indirectly via interaction with the basaltranscription apparatus (e.g. TFs), or by altering the accessibility of DNA to TFs via chromatinremodeling. Another type of regulatory proteins, protein kinases (PKs), function in signaltransduction pathways and alter the activity of target proteins by phosphorylating them. Thesethree important classes of regulatory proteins have been associated with numerous aspects ofplant growth and development (Gapper et al., 2014; Xu and Zhang, 2015), and response to bioticand abiotic stimuli (Mickelbart et al., 2015; Zhang et al., 2013). Effective and accurateidentification and classification of these genes is important for understanding their evolution,biological functions, and regulatory networks. Currently, more than 100 plant genomes havebeen sequenced and regulatory proteins have been systematically identified from several of theseplant genomes. Databases presenting these regulatory proteins, especially TFs, have beendeveloped, 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 beeninconsistent among different studies. For example, the PlantTFDB does not include TRs that arepresented in PlnTFDB. As another example, the ?forbidden? domain (a domain that the specificTF families should not contain) of the C2H2 family is annotated as an RNase_T domain inPlantTFDB, but as a PHD domain in PlnTFDB. Presently, while the collection of genomesequences is rapidly expanding, cataloged and annotated TFs/TRs vary across different databasesdue to inconsistent identification and characterization criteria with serious consequences forgenome scale and targeted analyses. Furthermore, in contrast to many studies focusing onspecific families of plant regulators, computational tools for identification and classification ofthese regulatory proteins on a genome scale are very limited.