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

• Autores: Zheng, Yi; Jiao, Chen; Sun, Honghe; Rosli, Hernan Guillermo; Pombo, Marina Alejandra; Zhang, Peifen; Banf, Michael; Dai, Xinbin; Martin, Gregory B.; Giovannoni, James J.; Zhao, Patrick X.; Rhee, Seung Y.; Fei, Zhangjun
• Año de publicación: 2016
• Idioma: inglés
• Tipo de recurso: artículo
• Materia: Itak; Database; Transcription Factors; Kinases
• Institución: Consejo Nacional de Investigaciones Científicas y Técnicas

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.
Fil: Zheng, Yi. Boyce Thompson Institute; Estados Unidos
Fil: Jiao, Chen. Boyce Thompson Institute; Estados Unidos
Fil: Sun, Honghe. Boyce Thompson Institute; Estados Unidos
Fil: Rosli, Hernan Guillermo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Fisiología Vegetal. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. Instituto de Fisiología Vegetal; Argentina. Boyce Thompson Institute; Estados Unidos
Fil: Pombo, Marina Alejandra. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Fisiología Vegetal. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. Instituto de Fisiología Vegetal; Argentina. Boyce Thompson Institute; Estados Unidos
Fil: Zhang, Peifen. Carnegie Institution for Science; Estados Unidos
Fil: Banf, Michael. Carnegie Institution for Science; Estados Unidos
Fil: Dai, Xinbin. Samuel Roberts Noble Foundation; Estados Unidos
Fil: Martin, Gregory B.. Boyce Thompson Institute; Estados Unidos. Cornell University; Estados Unidos
Fil: Giovannoni, James J.. Boyce Thompson Institute; Estados Unidos. Center for Agriculture and Health; Estados Unidos
Fil: Zhao, Patrick X.. Samuel Roberts Noble Foundation; Estados Unidos
Fil: Rhee, Seung Y.. Carnegie Institution for Science; Estados Unidos
Fil: Fei, Zhangjun. Boyce Thompson Institute; Estados Unidos. Center for Agriculture and Health; Estados Unidos