Limits...
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

An unrooted dendrogram of switchgrass AP2/ERF proteins. The deduced amino acid sequences were imported into MEGA6.0 program and aligned using MUSCLE program. The tree was constructed by a neighbor-joining method with bootstrap replicates of 5000. The families, subfamilies, and groups within each subfamilies are indicated in the tree. The list of switchgrass sequences used to construct this tree along with their gene identifier names are presented in Table S2 in Supplementary Material.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4507462&req=5

Figure 1: An unrooted dendrogram of switchgrass AP2/ERF proteins. The deduced amino acid sequences were imported into MEGA6.0 program and aligned using MUSCLE program. The tree was constructed by a neighbor-joining method with bootstrap replicates of 5000. The families, subfamilies, and groups within each subfamilies are indicated in the tree. The list of switchgrass sequences used to construct this tree along with their gene identifier names are presented in Table S2 in Supplementary Material.

Mentions: To confirm the classification and evaluate the sequence similarities between the switchgrass AP2/ERF TFs, a dendrogram was constructed by NJ method using the whole amino acid sequences of the proteins. The analysis showed distinct clustering of the proteins into specific groups and families as previously described in other species (Figure 1). Specifically, these clusters highlighted the distinction between the switchgrass AP2, ERF, and RAV families as well as between the ERF and DREB subfamilies. The ERF and DREB subfamilies were further subdivided into seven (groups V–XI) and four (I–IV) distinct groups, respectively. The cluster analysis also resolved the RAV protein family and the singleton into separate clusters, which was in accordance with the sequence similarities in the conserved domains as well as the presence of additional domains in the families/clusters.


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)

An unrooted dendrogram of switchgrass AP2/ERF proteins. The deduced amino acid sequences were imported into MEGA6.0 program and aligned using MUSCLE program. The tree was constructed by a neighbor-joining method with bootstrap replicates of 5000. The families, subfamilies, and groups within each subfamilies are indicated in the tree. The list of switchgrass sequences used to construct this tree along with their gene identifier names are presented in Table S2 in Supplementary Material.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 1: An unrooted dendrogram of switchgrass AP2/ERF proteins. The deduced amino acid sequences were imported into MEGA6.0 program and aligned using MUSCLE program. The tree was constructed by a neighbor-joining method with bootstrap replicates of 5000. The families, subfamilies, and groups within each subfamilies are indicated in the tree. The list of switchgrass sequences used to construct this tree along with their gene identifier names are presented in Table S2 in Supplementary Material.
Mentions: To confirm the classification and evaluate the sequence similarities between the switchgrass AP2/ERF TFs, a dendrogram was constructed by NJ method using the whole amino acid sequences of the proteins. The analysis showed distinct clustering of the proteins into specific groups and families as previously described in other species (Figure 1). Specifically, these clusters highlighted the distinction between the switchgrass AP2, ERF, and RAV families as well as between the ERF and DREB subfamilies. The ERF and DREB subfamilies were further subdivided into seven (groups V–XI) and four (I–IV) distinct groups, respectively. The cluster analysis also resolved the RAV protein family and the singleton into separate clusters, which was in accordance with the sequence similarities in the conserved domains as well as the presence of additional domains in the families/clusters.

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