Identification and molecular characterization of the switchgrass AP2/ERF transcription factor superfamily, and overexpression of PvERF001 for improvement of biomass characteristics for biofuel

Wuddineh, Wegi A.; Mazarei, Mitra; Turner, Geoffry B.; Sykes, Robert W.; Decker, Stephen R.; Davis, Mark F.

doi:10.3389/fbioe.2015.00101

Title: Identification and molecular characterization of the switchgrass AP2/ERF transcription factor superfamily, and overexpression of PvERF001 for improvement of biomass characteristics for biofuel

Journal Article · Mon Jul 20 00:00:00 EDT 2015 · Frontiers in Bioengineering and Biotechnology

DOI:https://doi.org/10.3389/fbioe.2015.00101· OSTI ID:1225355

Wuddineh, Wegi A. ^[1]; Mazarei, Mitra ^[1]; Turner, Geoffry B. ^[2]; Sykes, Robert W. ^[2]; Decker, Stephen R. ^[2]; Davis, Mark F. ^[2]

Univ. of Tennessee, Knoxville, TN (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); National Renewable Energy Lab. (NREL), Golden, CO (United States)

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. Furthermore, 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.

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Research Organization:: National Renewable Energy Laboratory (NREL), Golden, CO (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: AC36-08GO28308

OSTI ID:: 1225355

Report Number(s):: NREL/JA-5100-65049

Journal Information:: Frontiers in Bioengineering and Biotechnology, Vol. 3; Related Information: Frontiers in Bioengineering and Biotechnology; ISSN 2296-4185

Publisher:: Frontiers Research FoundationCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 42 works

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Sugar release and growth of biofuel crops are improved by downregulation of pectin biosynthesis Biswal, Ajaya K.; Atmodjo, Melani A.; Li, Mi Nature Biotechnology, Vol. 36, Issue 3 https://doi.org/10.1038/nbt.4067	journal	February 2018
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RAV transcription factors are essential for disease resistance against cassava bacterial blight via activation of melatonin biosynthesis genes Wei, Yunxie; Chang, Yanli; Zeng, Hongqiu Journal of Pineal Research, Vol. 64, Issue 1 https://doi.org/10.1111/jpi.12454	journal	December 2017
Biotechnological Strategies to Improve Plant Biomass Quality for Bioethanol Production Peña-Castro, Julián Mario; del Moral, Sandra; Núñez-López, Lizeth BioMed Research International, Vol. 2017 https://doi.org/10.1155/2017/7824076	journal	January 2017
Genome-wide identification, phylogeny and expression analysis of AP2/ERF transcription factors family in Brachypodium distachyon Cui, Licao; Feng, Kewei; Wang, Mengxing BMC Genomics, Vol. 17, Issue 1 https://doi.org/10.1186/s12864-016-2968-8	journal	August 2016
Insight into the AP2/ERF transcription factor superfamily in sesame and expression profiling of DREB subfamily under drought stress Dossa, Komivi; Wei, Xin; Li, Donghua BMC Plant Biology, Vol. 16, Issue 1 https://doi.org/10.1186/s12870-016-0859-4	journal	July 2016
Overexpression of a rice BAHD acyltransferase gene in switchgrass (Panicum virgatum L.) enhances saccharification Li, Guotian; Jones, Kyle C.; Eudes, Aymerick BMC Biotechnology, Vol. 18, Issue 1 https://doi.org/10.1186/s12896-018-0464-8	journal	September 2018
Development and use of a switchgrass (Panicum virgatum L.) transformation pipeline by the BioEnergy Science Center to evaluate plants for reduced cell wall recalcitrance Nelson, Richard S.; Stewart, C. Neal; Gou, Jiqing Biotechnology for Biofuels, Vol. 10, Issue 1 https://doi.org/10.1186/s13068-017-0991-x	journal	December 2017
Switchgrass (Panicum virgatum L.) promoters for green tissue-specific expression of the MYB4 transcription factor for reduced-recalcitrance transgenic switchgrass Liu, Wusheng; Mazarei, Mitra; Ye, Rongjian Biotechnology for Biofuels, Vol. 11, Issue 1 https://doi.org/10.1186/s13068-018-1119-7	journal	April 2018
Revealing the transcriptomic complexity of switchgrass by PacBio long-read sequencing Zuo, Chunman; Blow, Matthew; Sreedasyam, Avinash Biotechnology for Biofuels, Vol. 11, Issue 1 https://doi.org/10.1186/s13068-018-1167-z	journal	June 2018
Heteroexpression of Osa-miR319b improved switchgrass biomass yield and feedstock quality by repression of PvPCF5 Liu, Yanrong; Yan, Jianping; Wang, Kexin Biotechnology for Biofuels, Vol. 13, Issue 1 https://doi.org/10.1186/s13068-020-01693-0	journal	March 2020
Overexpression of the WOX gene STENOFOLIA improves biomass yield and sugar release in transgenic grasses and display altered cytokinin homeostasis Wang, Hui; Niu, Lifang; Fu, Chunxiang PLOS Genetics, Vol. 13, Issue 3 https://doi.org/10.1371/journal.pgen.1006649	journal	March 2017
Comparative Transcriptomic Analyses of Differentially Expressed Genes in Transgenic Melatonin Biosynthesis Ovine HIOMT Gene in Switchgrass Yuan, Shan; Guan, Cong; Liu, Sijia Frontiers in Plant Science, Vol. 7 https://doi.org/10.3389/fpls.2016.01613	journal	November 2016
Current Models for Transcriptional Regulation of Secondary Cell Wall Biosynthesis in Grasses Rao, Xiaolan; Dixon, Richard A. Frontiers in Plant Science, Vol. 9 https://doi.org/10.3389/fpls.2018.00399	journal	April 2018
Genetic engineering of grass cell wall polysaccharides for biorefining Bhatia, Rakesh; Gallagher, Joe A.; Gomez, Leonardo D. Plant Biotechnology Journal, Vol. 15, Issue 9 https://doi.org/10.1111/pbi.12764	journal	June 2017
Comparative transcriptome profiling of upland (VS16) and lowland (AP13) ecotypes of switchgrass Ayyappan, Vasudevan; Saha, Malay C.; Thimmapuram, Jyothi Plant Cell Reports, Vol. 36, Issue 1 https://doi.org/10.1007/s00299-016-2065-0	journal	November 2016
The Pivotal Role of Ethylene in Plant Growth Dubois, Marieke; Van den Broeck, Lisa; Inzé, Dirk Trends in Plant Science, Vol. 23, Issue 4 https://doi.org/10.1016/j.tplants.2018.01.003	journal	April 2018
Transgenic miR156 switchgrass in the field: growth, recalcitrance and rust susceptibility Baxter, Holly L.; Mazarei, Mitra; Dumitrache, Alexandru Plant Biotechnology Journal, Vol. 16, Issue 1 https://doi.org/10.1111/pbi.12747	journal	June 2017
RNA-seq Analysis of Overexpressing Ovine AANAT Gene of Melatonin Biosynthesis in Switchgrass Yuan, Shan; Huang, Yanhua; Liu, Sijia Frontiers in Plant Science, Vol. 7 https://doi.org/10.3389/fpls.2016.01289	journal	August 2016
Genome-Wide Identification of AP2/ERF Transcription Factors in Cauliflower and Expression Profiling of the ERF Family under Salt and Drought Stresses Li, Hui; Wang, Yu; Wu, Mei Frontiers in Plant Science, Vol. 8 https://doi.org/10.3389/fpls.2017.00946	journal	June 2017

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