In silico Analysis of Transcription Factor Repertoire and Prediction of Stress Responsive Transcription Factors in Soybean

Abstract

Sequence-specific DNA-binding transcription factors (TFs) are often termed as ‘master regulators’ which bind to DNA and either activate or repress gene transcription. We have computationally analysed the soybean genome sequence data and constructed a proper set of TFs based on the Hidden Markov Model profiles of DNA-binding domain families. Within the soybean genome, we identified 4342 loci encoding 5035 TF models which grouped into 61 families. We constructed a database named SoybeanTFDB () containing the full compilation of soybean TFs and significant information such as: functional motifs, full-length cDNAs, domain alignments, promoter regions, genomic organization and putative regulatory functions based on annotations of gene ontology (GO) inferred by comparative analysis with Arabidopsis. With particular interest in abiotic stress signalling, we analysed the promoter regions for all of the TF encoding genes as a means to identify abiotic stress responsive cis-elements as well as all types of cis-motifs provided by the PLACE database. SoybeanTFDB enables scientists to easily access cis-element and GO annotations to aid in the prediction of TF function and selection of TFs with functions of interest. This study provides a basic framework and an important user-friendly public information resource which enables analyses of transcriptional regulation in soybean.

Molecular Responses to Osmotic Stresses in Soybean

“…The release of a reference soybean genome sequence enables a quick survey of transcription factors in soybean (Mochida et al, 2009;Schmutz et al, 2010;Wang et al, 2010b). There are >4000 transcription factor gene loci occupying 6.56% of nonredundant gene loci in the soybean genome, more than a double of that in A. thaliana (~ 1900 out of 27235, ~7%) and rice (~2000 out of 56797, ~3.5%; Mochida et al, 2009). Categorizing the annotated loci according to GO terms suggests that more than 500 transcription factors in soybean would probably respond to osmotic stresses (Mochida et al, 2009).…”

“…There are >4000 transcription factor gene loci occupying 6.56% of nonredundant gene loci in the soybean genome, more than a double of that in A. thaliana (~ 1900 out of 27235, ~7%) and rice (~2000 out of 56797, ~3.5%; Mochida et al, 2009). Categorizing the annotated loci according to GO terms suggests that more than 500 transcription factors in soybean would probably respond to osmotic stresses (Mochida et al, 2009). There are rapid accumulations of information on soybean transcription factors and their putative functions related to osmotic stresses (Tian et al, 2004;Mochida et al, 2009;Schmutz et al, 2010;Wang et al, 2010b).…”

“…Categorizing the annotated loci according to GO terms suggests that more than 500 transcription factors in soybean would probably respond to osmotic stresses (Mochida et al, 2009). There are rapid accumulations of information on soybean transcription factors and their putative functions related to osmotic stresses (Tian et al, 2004;Mochida et al, 2009;Schmutz et al, 2010;Wang et al, 2010b). A summary of the recent findings is presented below and in Table 1. AP2/ERF AP2/ERF transcription factors can be classified into 5 subfamilies including the AP2 (APETALA2), ERF (ethylene-responsive transcription factor), DREB (dehydration-responsive element-binding protein), RAV (related to ABI3/VP1), and Soloist (Sakuma et al, 2002;Zhuang et al, 2009) depending on the number of AP2/EFR domain.…”

“…A summary of the recent findings is presented below and in Table 1. AP2/ERF AP2/ERF transcription factors can be classified into 5 subfamilies including the AP2 (APETALA2), ERF (ethylene-responsive transcription factor), DREB (dehydration-responsive element-binding protein), RAV (related to ABI3/VP1), and Soloist (Sakuma et al, 2002;Zhuang et al, 2009) depending on the number of AP2/EFR domain. More than 380 AP2/ERF genes are present in the soybean genome (Mochida et al, 2009;Wang et al, 2010b) while only a few of them have been characterized (Gao et al, 2005;Li et al, 2005;Chen et al, 2006;Chen et al, 2007;Mazarei et al, 2007;Wang et al, 2008;Zhang et al, 2008b;Chen et al, 2009a;Zhang et al, 2009a;Zhang et al, 2009b;Zhuang et al, 2009;El Ouakfaoui et al, 2010;Jin et al, 2010). More than 10 members of the gene family encoding DREB transcription factors present in the soybean genome (Phang et al, 2008), and 7 of the GmDREB genes are induced by ABA, salt, drought, and/or cold stress (Table 1) (Gao et al, 2005;Li et al, 2005;Chen et al, 2006;Chen et al, 2007;Chen et al, 2009a;Jin et al, 2010).…”

Identification and prediction of abiotic stress responsive transcription factors involved in abiotic stress signaling in soybean

“…psc.riken.jp). 21 Given the fact that at the present time, the stress-related expression data, which would aid in selection of stress responsive TFs for further functional studies and genetic engineering, are not yet available for most of the soybean TF genes, it was important to find an approach to systematically identify the stress responsive TFs for further characterization and functional analyses in a reliable manner. Recent studies have substantiated that sequence similarity-based clustering of the members of several TF families correlates with their function.…”