Transcriptional regulation of the paper mulberry under cold stress as revealed by a comprehensive analysis of transcription factors

Abstract

BackgroundSeveral studies have focused on cold tolerance in multiple regulated levels. However, a genome-scale molecular analysis of the regulated network under the control of transcription factors (TFs) is still lacking, especially for trees. To comprehensively identify the TFs that regulate cold stress response in the paper mulberry and understand their regulatory interactions, transcriptomic data was used to assess changes in gene expression induced by exposure to cold.ResultsResults indicated that 794 TFs, belonging to 47 families and comprising more than 59% of the total TFs of this plant, were involved in the cold stress response. They were clustered into three groups, namely early, intermediate and late responsive groups which contained 95, 550 and 149 TFs, respectively. Among of these differentially expressed TFs, one bHLH, two ERFs and three CAMTAs were considered to be the key TFs functioning in the primary signal transduction. After that, at the intermediate stage of cold stress, there were mainly two biological processes that were regulated by TFs, namely cold stress resistance (including 5 bHLH, 14 ERFs, one HSF, 4 MYBs, 3 NACs, 11 WRKYs and so on) and growth and development of lateral organ or apical meristem (including ARR-B, B3, 5 bHLHs, 2 C2H2, 4 CO-like, 2 ERF, 3 HD-ZIP, 3 YABBYs, G2-like, GATA, GRAS and TCP). In late responsive group, 3 ARR-B, C3H, 6 CO-like, 2 G2-like, 2 HSFs, 2 NACs and TCP. Most of them presented the up-regulated expression at 12 or 24 hours after cold stress implied their important roles for the new growth homeostasis under cold stress.ConclusionsOur study identified the key TFs that function in the regulatory cascades mediating the activation of downstream genes during cold tress tolerance in the paper mulberry. Based on the analysis, we found that the AP2/ERF, bHLH, MYB, NAC and WRKY families might play the central and significant roles during cold stress response in the paper mulberry just as in other species. Meanwhile, many other TF families previously reported as involving in regulation of growth and development, including ARF, DBB, G2-like, GRF, GRAS, LBD, WOX and YAABY exhibited their important potential function in growth regulation under cold stress.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0489-2) contains supplementary material, which is available to authorized users.

Overexpression of the class I homeodomain transcription factor TaHDZipI‐5 increases drought and frost tolerance in transgenic wheat

“…Regulation of HD‐Zip I gene expression by low temperatures was demonstrated for Arabidopsis (Cabello et al ., ), tomato (Zhang et al ., ), paper mulberry (Peng et al ., ), sunflower (Cabello et al ., ), rice (Zhang et al ., ) and wheat (Harris et al ., ). The overexpression of α‐clade HD‐Zip class I TFs conferred cold/frost tolerance to transgenic Arabidopsis and barley (Cabello et al ., ; Kovalchuk et al ., ); however, the influence on the overexpression of monocot‐specific γ‐clade members on cold or frost tolerance of transgenic plants remains to be determined.…”

“…An attractive target for this approach is the family of homeodomain-leucine zipper (HD-Zip) TFs, which contains proteins regulating plant development after plants are exposed to environmental stimuli and stresses (Brandt et al, 2014;Harris et al, 2011;Perotti et al, 2017). All HD-Zip TFs possess a highly conserved homeodomain (HD) and leucine zipper (Zip or LZ) motifs (Ariel et al, 2007;Harris et al, 2016;Mattsson et al, 1992;Ruberti et al, 1991;Davis, 1992, 1994).…”

The complete chloroplast genome of an economic and ecological plant, paper mulberry (Broussonetia kazinoki × Broussonetia papyifera)

“…The abundant flavonoids in paper mulberry have long been used in Chinese medicine (Sun et al 2012). In terms of ecological values, the tree grow fast and have strong tolerance to cold, drought and salt (Li et al 2011;Sun et al 2014;Peng et al 2015), which can be planted as a pioneer tree in ecological degradation area. Thus, it is useful to know more genetic information about paper mulberry to reveal the mechanism of evolution or adoption.…”

Norway spruce deploys tissue specific canonical responses to acclimate to cold

“…A network model of inferred transcriptional regulations of COR genes was built using an approach previously used to identify putative plant cold acclimation pathways and key TFs in Arabidopsis and rice (Chawade et al, 2007; Lindlof et al, 2009). The analyzed motifs were consensus target sequences for ERF, NAC, MYB, bZIP, bHLH, AP2, DRE, LBD and WRKY families, which have previously been associated with plant cold stress (Chawade et al, 2007; Peng et al, 2015). For each motif, confidence intervals (CI) were obtained (Table 1) and used as a criterion of over-representation.…”