Abstract
The APETALA2/ethylene response factor (AP2/ERF) superfamily of transcription factors (TFs) plays essential roles in the regulation of various growth and developmental programs including stress responses. Members of these TFs in other plant species have been implicated to play a role in the regulation of cell wall biosynthesis. Here, we identified a total of 207 AP2/ERF TF genes in the switchgrass genome and grouped into four gene families comprised of 25 AP2-, 121 ERF-, 55 DREB (dehydration responsive element binding)-, and 5 RAV (related to API3/VP) genes, as well as a singleton gene not fitting any of the above families. The ERF and DREB subfamilies comprised seven and four distinct groups, respectively. Analysis of exon/intron structures of switchgrass AP2/ERF genes showed high diversity in the distribution of introns in AP2 genes versus a single or no intron in most genes in the ERF and RAV families. The majority of the subfamilies or groups within it were characterized by the presence of one or more specific conserved protein motifs. In silico functional analysis revealed that many genes in these families might be associated with the regulation of responses to environmental stimuli via transcriptional regulation of the response genes. Moreover, these genes had diverse endogenous expression patterns in switchgrass during seed germination, vegetative growth, flower development, and seed formation. Interestingly, several members of the ERF and DREB families were found to be highly expressed in plant tissues where active lignification occurs. These results provide vital resources to select candidate genes to potentially impart tolerance to environmental stress as well as reduced recalcitrance. Overexpression of one of the ERF genes (PvERF001) in switchgrass was associated with increased biomass yield and sugar release efficiency in transgenic lines, exemplifying the potential of these TFs in the development of lignocellulosic feedstocks with improved biomass characteristics for biofuels.
Highlights
Switchgrass (Panicum virgatum) is an outcrossing perennial C4 grass known for its vigorous growth and wide adaptability and, is being developed as a candidate lignocellulosic biofuel feedstock (Yuan et al, 2008)
We report the identification of 207 APETALA2/ethylene response factor (AP2/ERF) transcription factors (TFs) genes in the switchgrass genome
Amino acid sequence similarities within the conserved AP2 domain between these proteins and previously characterized AP2/ERF TFs from rice and Arabidopsis along with the presence of conserved B3 domain suggest that these proteins might be categorized as putative AP2/ERF TFs
Summary
Switchgrass (Panicum virgatum) is an outcrossing perennial C4 grass known for its vigorous growth and wide adaptability and, is being developed as a candidate lignocellulosic biofuel feedstock (Yuan et al, 2008). The feasibility of commercial production of liquid transportation biofuel from switchgrass biomass is hampered by biomass recalcitrance (the resistance of cell wall to enzymatic breakdown into simple sugars). Substantial progress has been made in engineering the switchgrass lignin biosynthesis pathway to reduce lignin content and/or modify its composition (Fu et al, 2011a,b; Shen et al, 2012, 2013a,b; Baxter et al, 2014, 2015). Overexpression of transcription factors (TFs), such as switchgrass MYB4, has been shown to circumvent this inhibitory effect while leading to significantly reduced biomass recalcitrance and improved ethanol production (Shen et al, 2012, 2013b; Baxter et al, 2015)
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