Tobacco Transcription Factors: Novel Insights into Transcriptional Regulation in the Solanaceae      

Abstract

Tobacco (Nicotiana tabacum) is a member of the Solanaceae, one of the agronomically most important groups of flowering plants. We have performed an in silico analysis of 1.15 million gene-space sequence reads from the tobacco nuclear genome and report the detailed analysis of more than 2,500 tobacco transcription factors (TFs). The tobacco genome contains at least one member of each of the 64 well-characterized TF families identified in sequenced vascular plant genomes, indicating that evolution of the Solanaceae was not associated with the gain or loss of TF families. However, we found notable differences between tobacco and non-Solanaceae species in TF family size and evidence for both tobacco-and Solanaceae-specific subfamily expansions. Compared with TF families from sequenced plant genomes, tobacco has a higher proportion of ERF/AP2, C2H2 zinc finger, homeodomain, GRF, TCP, zinc finger homeodomain, BES, and STERILE APETALA (SAP) genes and novel subfamilies of BES, C2H2 zinc finger, SAP, and NAC genes. The novel NAC subfamily, termed TNACS, appears restricted to the Solanaceae, as they are absent from currently sequenced plant genomes but present in tomato (Solanum lycopersicum), pepper (Capsicum annuum), and potato (Solanum tuberosum). They constitute approximately 25% of NAC genes in tobacco. Based on our phylogenetic studies, we predict that many of the more than 50 tobacco group IX ERF genes are involved in jasmonate responses. Consistent with this, over two-thirds of group IX ERF genes tested showed increased mRNA levels following jasmonate treatment. Our data are a major resource for the Solanaceae and fill a void in studies of TF families across the plant kingdom.

APETALA2/ETHYLENE RESPONSE FACTOR and basic helix–loop–helix tobacco transcription factors cooperatively mediate jasmonate‐elicited nicotine biosynthesis

“…Twenty-four hours after transfection with hairpin (hp) gene silencing constructs, BY-2 protoplasts were elicited with MeJA and fLUC reporter activity was measured after incubation for another 24 h. The ProNsPMT2 and ProQPRT2 activities were slightly and strongly reduced, respectively, upon transfection with the ORC1 hp construct (Figure 5a), suggesting that NIC2 AP2/ERF factors including ORC1 are involved in the MeJA-mediated activation of nicotine biosynthesis in tobacco and consistent with the effects observed by RNA interference (RNAi)-mediated suppression of the NIC2 AP2/ ERF genes in tobacco plants (Shoji et al, 2010). The action of ORC1 may be invoked, at least in part, through MeJA-mediated transcriptional induction of the ORC1 gene (Goossens et al, 2003), together with that of the other NIC2 ERF and the MYC2-like bHLH factors (Rushton et al, 2008;Shoji et al, 2010;Todd et al, 2010). In addition, however, we noted that in transient expression assays, transactivation of ProNsPMT2 and ProQPRT2 by ORC1 was augmented with MeJA elicitation (Figure 5b), suggesting that the JA signal enhances the transactivation potential of the ORC1 protein.…”

“…The phylogeny of the JA-responsive AP2/ERF and bHLH factors (Rushton et al, 2008), and the outcome of various functional screens in which multiple isoforms of both TF families were shown to positively regulate nicotine biosynthesis (De Sutter et al, 2005;Todd et al, 2010;Shoji et al, 2010), suggests that tobacco plants have developed a daunting repertoire of transcriptional regulators to control their secondary metabolism. Yet it is striking that for virtually none of the bHLH nor the NIC2 ERF activators identified so far, expression is exclusively confined to the roots, and that for many the corresponding transcripts are even encountered in all organs tested (Todd et al, 2010;Shoji et al, 2010;this study).…”

“…In agreement with these findings, we previously showed that two JA-inducible AP2/ERF TFs from tobacco, ORC1 and JAP1, positively regulate the PMT promoter in a protoplast-based transient expression assay (Goossens et al, 2003;De Sutter et al, 2005). ORC1 and JAP1 both belong, similar to all the NIC2 AP2/ERFs, to group IX of ERF genes, and are also known as ERF221 (one of the NIC2 AP2/ERFs in clade 2-1) and ERF10 (clade 1), respectively (Rushton et al, 2008;Shoji et al, 2010).…”

“…In tobacco, the ERF family of AP2 domain TFs consists of at least 239 members (Rushton et al, 2008), and very recently it has been established that AP2/ERF factors also play a prominent regulatory role in nicotine biosynthesis. In fact, it turned out that the NIC2 locus, one of the long-sought regulatory NIC loci that positively regulate nicotine biosynthesis in tobacco, comprised at least seven clustered AP2/ ERF encoding genes (Shoji et al, 2010).…”

A systems biology perspective on the role of WRKY transcription factors in drought responses in plants

“…Based on the number of wRKY domains in the protein and structure of the zinc finger motif the whole family was divided into three different groups (eulgem et al 2000). Detailed phylogenetic analyses subsequently revealed a distribution of the wRKY family in higher plants into groups I, IIa+b, IIc, IId+e and III (Rushton et al 2008a;Zhang and wang 2005).…”