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Identification and Molecular Characterization of the Switchgrass AP2/ERF Transcription Factor Superfamily, and Overexpression of PvERF001 for Improvement of Biomass Characteristics for Biofuel.

Wuddineh WA, Mazarei M, Turner GB, Sykes RW, Decker SR, Davis MF, Stewart CN - Front Bioeng Biotechnol (2015)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Sciences, University of Tennessee , Knoxville, TN , USA ; Bioenergy Science Center, Oak Ridge National Laboratory , Oak Ridge, TN , USA.

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.

No MeSH data available.


Related in: MedlinePlus

The schematic representation of protein and gene structures of switchgrass ERF subfamily. (A) Distribution of conserved motifs within the deduced amino acid sequences as determined by MEME tool (Bailey and Elkan, 1994). The colored boxes represent the conserved motifs. (B) The gene features as visualized by the gene structure display server (Guo et al., 2007). The coding DNA sequence (CDS) and the untranslated regions (UTR) are shown by filled dark-blue and red boxes, respectively. The introns are shown by thick black lines. The splicing phases of the introns are indicated by numbers. The Roman numerals indicate the group of the genes within the subfamily.
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Figure 2: The schematic representation of protein and gene structures of switchgrass ERF subfamily. (A) Distribution of conserved motifs within the deduced amino acid sequences as determined by MEME tool (Bailey and Elkan, 1994). The colored boxes represent the conserved motifs. (B) The gene features as visualized by the gene structure display server (Guo et al., 2007). The coding DNA sequence (CDS) and the untranslated regions (UTR) are shown by filled dark-blue and red boxes, respectively. The introns are shown by thick black lines. The splicing phases of the introns are indicated by numbers. The Roman numerals indicate the group of the genes within the subfamily.

Mentions: To complement the cluster analysis-based classification, the exon–intron structures of AP2/ERF genes were evaluated. The schematic representations of protein and gene structures of switchgrass AP2/ERF superfamily are presented in Figure 2 (ERF), Figure 3 (DREB), and Figure 4 (AP2, RAV, and Singleton). The ORF lengths of these genes vary from 394 bp for the shortest gene to 5409 bp for the longest gene. Analysis of their gene structure showed highly diverse distribution of intron regions within the ORF of the different gene groups or families. The majority of genes belonging to ERF and DREB subfamilies and all but one of the RAV genes appeared to be intronless. Only nine DREB genes (16%) belonging to group I, III, and VI had a single intron in their gene structures. Among ERF genes, 45 (37%) had a single intron in their ORF while eight genes had two and three of them with three introns in its ORF. On the other hand, genes in the AP2 family contained a higher number of introns; ranging from 1 to 10. Only one gene in the AP2 family had a single intron while majority of the genes had more than five introns. The position and state of the introns in the ORF of ERF family genes belonging to groups V, VII, and X show high functional conservation. For instance, about half of the genes belonging to phylogenetic group V in the ERF family showed highly conserved intron positions with an intron phase of two, meaning the location of the intron is found between the second and third nucleotides in the codon. Similarly, the intron positions and splicing phases seems conserved in group VII of the ERF subfamily (Figures 2–4).


Identification and Molecular Characterization of the Switchgrass AP2/ERF Transcription Factor Superfamily, and Overexpression of PvERF001 for Improvement of Biomass Characteristics for Biofuel.

Wuddineh WA, Mazarei M, Turner GB, Sykes RW, Decker SR, Davis MF, Stewart CN - Front Bioeng Biotechnol (2015)

The schematic representation of protein and gene structures of switchgrass ERF subfamily. (A) Distribution of conserved motifs within the deduced amino acid sequences as determined by MEME tool (Bailey and Elkan, 1994). The colored boxes represent the conserved motifs. (B) The gene features as visualized by the gene structure display server (Guo et al., 2007). The coding DNA sequence (CDS) and the untranslated regions (UTR) are shown by filled dark-blue and red boxes, respectively. The introns are shown by thick black lines. The splicing phases of the introns are indicated by numbers. The Roman numerals indicate the group of the genes within the subfamily.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4507462&req=5

Figure 2: The schematic representation of protein and gene structures of switchgrass ERF subfamily. (A) Distribution of conserved motifs within the deduced amino acid sequences as determined by MEME tool (Bailey and Elkan, 1994). The colored boxes represent the conserved motifs. (B) The gene features as visualized by the gene structure display server (Guo et al., 2007). The coding DNA sequence (CDS) and the untranslated regions (UTR) are shown by filled dark-blue and red boxes, respectively. The introns are shown by thick black lines. The splicing phases of the introns are indicated by numbers. The Roman numerals indicate the group of the genes within the subfamily.
Mentions: To complement the cluster analysis-based classification, the exon–intron structures of AP2/ERF genes were evaluated. The schematic representations of protein and gene structures of switchgrass AP2/ERF superfamily are presented in Figure 2 (ERF), Figure 3 (DREB), and Figure 4 (AP2, RAV, and Singleton). The ORF lengths of these genes vary from 394 bp for the shortest gene to 5409 bp for the longest gene. Analysis of their gene structure showed highly diverse distribution of intron regions within the ORF of the different gene groups or families. The majority of genes belonging to ERF and DREB subfamilies and all but one of the RAV genes appeared to be intronless. Only nine DREB genes (16%) belonging to group I, III, and VI had a single intron in their gene structures. Among ERF genes, 45 (37%) had a single intron in their ORF while eight genes had two and three of them with three introns in its ORF. On the other hand, genes in the AP2 family contained a higher number of introns; ranging from 1 to 10. Only one gene in the AP2 family had a single intron while majority of the genes had more than five introns. The position and state of the introns in the ORF of ERF family genes belonging to groups V, VII, and X show high functional conservation. For instance, about half of the genes belonging to phylogenetic group V in the ERF family showed highly conserved intron positions with an intron phase of two, meaning the location of the intron is found between the second and third nucleotides in the codon. Similarly, the intron positions and splicing phases seems conserved in group VII of the ERF subfamily (Figures 2–4).

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Sciences, University of Tennessee , Knoxville, TN , USA ; Bioenergy Science Center, Oak Ridge National Laboratory , Oak Ridge, TN , USA.

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.

No MeSH data available.


Related in: MedlinePlus