Splice variant of the SND1 transcription factor is a dominant negative of SND1 members and their regulation in Populus trichocarpa

Abstract

Secondary Wall-Associated NAC Domain 1s (SND1s) are transcription factors (TFs) known to activate a cascade of TF and pathway genes affecting secondary cell wall biosynthesis (xylogenesis) in Arabidopsis and poplars. Elevated SND1 transcriptional activation leads to ectopic xylogenesis and stunted growth. Nothing is known about the upstream regulators of SND1. Here we report the discovery of a stem-differentiating xylem (SDX)-specific alternative SND1 splice variant, PtrSND1-A2 IR , that acts as a dominant negative of SND1 transcriptional network genes in Populus trichocarpa. PtrSND1-A2 IR derives from PtrSND1-A2, one of the four fully spliced PtrSND1 gene family members (PtrSND1-A1, -A2, -B1, and -B2). Each full-size PtrSND1 activates its own gene, and all four full-size members activate a common MYB gene (PtrMYB021). PtrSND1-A2 IR represses the expression of its PtrSND1 member genes and PtrMYB021. Repression of the autoregulation of a TF family by its only splice variant has not been previously reported in plants. PtrSND1-A2 IR lacks DNA binding and transactivation abilities but retains dimerization capability. PtrSND1-A2 IR is localized exclusively in cytoplasmic foci. In the presence of any full-size PtrSND1 member, PtrSND1-A2 IR is translocated into the nucleus exclusively as a heterodimeric partner with full-size PtrSND1s. Our findings are consistent with a model in which the translocated PtrSND1-A2 IR lacking DNA-binding and transactivating abilities can disrupt the function of full-size PtrSND1s, making them nonproductive through heterodimerization, and thereby modulating the SND1 transcriptional network. PtrSND1-A2 IR may contribute to transcriptional homeostasis to avoid deleterious effects on xylogenesis and plant growth.

SND1 Transcription Factor-Directed Quantitative Functional Hierarchical Genetic Regulatory Network in Wood Formation in Populus trichocarpa

“…Understanding the regulatory hierarchy of wood formation will offer novel and more precise genetic approaches to improve the productivity of forest trees. Secondary wall-associated NAC domain (SND) and vascular-related NAC domain (VND) proteins are transcription factors (TFs) known to regulate TF and pathway genes affecting secondary cell wall biosynthesis (wood formation) in Populus spp (Ohtani et al, 2011;Zhong et al, 2011;Li et al, 2012). However, little is known at the genome-wide level about the regulatory target genes, their quantitative causal relationships, or their regulatory hierarchy.…”

“…The challenge is that woody plant tissues are generally resistant to protoplast isolation (Teulieres et al, 1991;Manders et al, 1992;Gomez-Maldonado et al, 2001;Sun et al, 2009;Tang et al, 2010;Chen et al, 2011;Li et al, 2012). Even for amenable woody plant tissues, protoplast isolation has never before been designed for yield and quality adequate for transgenesis, transcriptome and chromatin enrichment studies.…”

“…While TFs typically act cooperatively and combinatorially on their cis-regulatory DNA targets for gene expression (Müller, 2001; Levine and Tjian, 2003;Chen and Rajewsky, 2007;Hobert, 2008), a single TF may also target hundreds of genes (Chen and Rajewsky, 2007;Kaufmann et al, 2009;Demura and Ye, 2010;Huang et al, 2012;Li et al, 2012). Many TFs also target their own genes (autoactivation or repression) (Becskei and Serrano, 2000;Wray et al, 2003;Li et al, 2012).…”

“…Many TFs also target their own genes (autoactivation or repression) (Becskei and Serrano, 2000;Wray et al, 2003;Li et al, 2012). Interactions between a TF and its direct targets constitute a regulatory hierarchy.…”

“…Using Populus trichocarpa protoplasts from stem-differentiating xylem (SDX) as a model, we have begun to describe the SND/ VND-directed functional hGRN for wood formation, beginning with the hGRN associated with Secondary Wall-Associated NAC Domain 1s (Ptr-SND1-B1) (Li et al, 2012). Here, we report the establishment of an efficient SDX protoplast system for monitoring genome-wide Ptr-SND1-B1-induced gene transactivation responses and a novel computational method for constructing a hierarchical TF-DNA network.…”