Progress 01/01/07 to 12/31/11
Outputs
OUTPUTS: Transcription factors are proteins that regulate gene expression. NAC domain (NAC) transcription factors comprise a large family of plant-specific transcription factors that regulate genes involved in many aspects of plant growth and development. Recent work by our lab and other labs in the U.S. and Japan has revealed that a small subset of these NACs are regulators of xylem differentiation. Xylem is the wood-forming tissue in plants. Understanding how trees produce wood is important to our ability to increase plant biomass and biofuels production. Some NACs promote xylem differentiation while others repress xylem differentiation. Our investigations focus on NACs that repress xylem differentation. During this project we conducted laboratory, greenhouse and field trials for evaluating transgenic poplars overexpressing a poplar NAC protein, PtNAC154, that promotes bark accumulation and represses wood accumulation. We also prepared transgenic poplar in which PtNAC154 was silenced and these plants will be evaluated in field trials beginning in fall 2013. Proteins function in part through their interactions with other proteins. We recently identified a protein, RBR, that interacts with another negative regulator of wood formation, XND1. This XND1-interacting protein is well known as a key regulator of cell proliferation and differentiation, and we are currently determining how RBR impacts wood formation through its interaction with XND1. The most recent findings regarding protein-protein interactions relevant to wood formation were presented at the annual Plant and Animal Genome meeting, January 14-18, 2012, San Diego, CA. PARTICIPANTS: Eric Beers, PI, directed the project, analyzed data, and wrote publications. He also collaborated with Amy Brunner, Department of Forest Resources and Environmental Conservation, Virginia Tech, in the training of graduate students in poplar tissue culture for the creation of transgenic poplar for high-level expression of transcription factors. During the project, 14 undergraduate students and 2 graduate students were trained in methods of poplar research. Three postdoctorals performed experiments required for characterizations of transcription factors associated with wood formation. One graduate student characterized RNA-mediated regulation in apple trees. TARGET AUDIENCES: The principal target audience consisted of plant scientists studying growth and development of trees in general and the differentiation of vascular tissues in particular. The secondary audience comprised undergraduate and graduate students and postdoctoral researchers being trained in molecular biology and functional genomics relevant to tree research. Finally, in the classroom with both undergraduate and graduate students, project results were used to illustrate fundamental concepts in plant biology and plant biotechnology. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
As an increasingly important model for plant cellulosic biomass production, poplar is an important component of future efforts to increase biofuels production. Advancing our knowledge and increasing productivity in this area depends on increasing the numbers of scientists trained in biomass research methods. During this project, 14 undergraduate students and 2 graduate students were trained in methods of poplar research. Three postdoctorals performed experiments required for characterizations of transcription factors associated with wood formation. The results of this training and research activity were presented in 7 peer-reviewed publications (including 1 invited opinion article on classification of plant programmed cell death and 1 invited and peer-reviewed review on the role of proteases in vascular tissue development) and 1 book chapter. Results were presented by the principle investigator, postdoctorals and graduate students at 7 national and international meetings.
Publications
- Xia R, Zhu H, An Y, Beers EP, Liu Z (2012) Apple miRNAs and tasiRNAs with novel regulatory networks. Genome Biology. http://genomebiology.com/2012/13/6/R47
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Progress 10/01/10 to 09/30/11
Outputs
OUTPUTS: Transcription factors are proteins that regulate gene expression. NAC domain (NAC) transcription factors comprise a large family of plant-specific transcription factors that regulate genes involved in many aspects of plant growth and development. Recent work by our lab and other labs in the U.S. and Japan has revealed that a small subset of these NACs are regulators of xylem differentiation. Xylem is the wood-forming tissue in plants. Understanding how plants produce wood is important to our ability to increase plant biomass and biofuels production. Some NACs promote xylem differentiation while others repress xylem differentiation. Our investigations focus on NACs that repress xylem differentation. During this reporting period we began field trials for evaluating transgenic poplars overexpressing a poplar NAC protein, PtNAC154, that promotes bark accumulation and represses wood accumulation. Complementary experiments are underway to test the hypothesis that silencing this negative regulator will enhance wood production. Proteins function in part through their interactions with other proteins. We recently identified a protein that interacts with another negative regulator of wood formation, XND1. This XND1-interacting protein is an important regulator of cell proliferation and differentiation, and we are currently determing how this protein impacts wood formation through its interaction with XND1. In addition to publications reviewing the role of programmed cell death in wood formation, results were presented orally to members of the Molecular Plant Sciences Graduate Program at Virginia Tech. Findings were also presented at the First International Plant Protease Conference in Hemavan, Sweden, 10-14 April, 2011, and the annual meeting of the American Society of Plant Biologists in Minneapolis, MN, August, 2011. PARTICIPANTS: Eric Beers, PI, directed the project, analyzed data, and wrote publications. He also collaborated with Amy Brunner, Department of Forest Resources and Environmental Conservation, Virginia Tech, in the training of graduate students in poplar tissue culture for the creation of transgenic poplar for high-level expression of transcription factors. During the current reporting period, three undergraduate students and one graduate student were trained in methods of poplar research. Two postdoctorals performed experiments required for characterizations of transcription factors associated with wood formation. TARGET AUDIENCES: The principal target audience consisted of plant scientists studying the differentiation of vascular tissues and in particular the formation of wood (xylem). The secondary audience comprised undergraduate and graduate students and postdoctoral researchers being trained in poplar experimental biology. Finally, in the classroom with both undergraduate and graduate students, project results were used to illustrate fundamental concepts in plant biology and plant biotechnology. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
As an increasingly important model for plant cellulosic biomass production, poplar is an important component of future efforts to increase biofuels production. Advancing our knowledge and increasing productivity in this area depends on increasing the numbers of scientists trained in biomass research methods. During the current reporting period, three undergraduate students and one graduate student were trained in methods of poplar research. Two postdoctorals performed experiments required for characterizations of transcription factors associated with wood formation. The results of this training and research activity included one invited opinion article on classification of plant programmed cell death and one invited and peer-reviewed review on the role of proteases in vascular tissue development. One graduate student presented results at the annual meeting of the American Society of Plant Biologists in Minneapolis, MN, August, 2011.
Publications
- van Doorn WG, Beers EP. Dangl JL et al. (19 authors) (2011) Morphological classification of plant cell deaths. Cell Death and Differentiation 18: 1241-1246.
- Petzold HE, Zhao M, Beers EP (2011) Expression and functions of proteases in vascular tissue (2011) Physiologia Plantarum (In Press).
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Progress 10/01/09 to 09/30/10
Outputs
OUTPUTS: Transcription factors (TFs) are proteins that regulate gene expression. NAC domain (NAC) TFs comprise a large family of plant-specific TFs that regulate genes involved in many aspects of plant growth and development. A subset of these NACs are regulators of xylem differentiation. Xylem is the wood-forming tissue in plants. Understanding how plants produce wood is important to our ability to increase plant biomass and biofuels production. Some NACs promote xylem differentiation while others repress xylem differentiation. During this reporting period our investigations focus on poplar NACs that are most closely related to the Arabidopsis genes XYLEM NAC DOMAIN1 (XND1) and SECONDARY WALL NAC DOMAIN3 (SND3). The poplar genome contains four XND1-like genes and four SND3-like genes. During this reporting period we published our analysis of these eight poplar NACs. We found that transgenic poplar plants expressing high levels of XND1 produced less xylem vessels and no phloem fibers, while transgenic poplar plants overexpressing one of the poplar SND3-like genes produced more inner and outer bark than wild type controls. In addition to publishing this work, results were presented orally to members of the Molecular Plant Sciences Graduate Program at Virginia Tech and at the Ninth International Plant Molecular Biology Congress in St. Louis, MO. PARTICIPANTS: Eric Beers, PI, directed project, analyzed data, and wrote publications in collaboration with Amy Brunner, Department of Forest Resources and Environmental Conservation, Virginia Tech. Dr. Brunner also provided training for graduate students in poplar tissue culture for the creation of transgenic poplar for high-level expression of transcription factors. During the current reporting period, five undergraduate students and two graduate students were trained in methods of poplar research. Two postdoctorals performed experiments required for characterizations of transcription factors associated with wood formation. TARGET AUDIENCES: The principal target audience consisted of plant scientists studying wood formation. The secondary audience was undergraduate and graduate students and postdoctoral researchers being trained in poplar experimental biology. Finally, in the classroom with both undergraduate and graduate students, project results were used to illustrate fundamental concepts in plant biology and plant biotechnology. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
As an increasingly important model for plant cellulosic biomass production, poplar is an important component of future efforts to increase biofuels production. Advancing our knowledge in this area depends on increasing the numbers of graduate students and postdoctoral researchers trained in biomass research methods. During the current reporting period, two graduate students and five undergraduate students were trained in poplar gene expression analysis and genomics and poplar tissue culture. Additionally, one graduate student was trained in the use of poplar genomic resources and methods for identifying interacting proteins important to wood formation. The result of this training and research activity was a peer-reviewed original research publication characterizing expression and function of eight poplar NAC domain transcription factors.
Publications
- Grant, E.H., Fujino, T., Beers, E.P., and Brunner, A.M. (2010). Characterization of NAC domain transcription factors implicated in control of vascular cell differentiation in Arabidopsis and poplar, Planta, 232: 337-352.
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Progress 10/01/08 to 09/30/09
Outputs
OUTPUTS: Transcription factors (TFs) are proteins that regulate gene expression. NAC domain (NAC) TFs comprise a large family of plant-specific TFs that regulate genes involved in many aspects of plant growth and development. A small subset of these NACs are regulators of xylem differentiation. Xylem is the wood-forming tissue in plants. Understanding how plants produce wood is important to our ability to increase plant biomass and biofuels production. Some NACs promote xylem differentiation while others repress xylem differentiation. Our investigations focus on a subset of poplar NACs that are most closely related to the Arabidopsis gene XYLEM NAC DOMAIN1 (XND1), a gene shown by my lab to be able to repress xylem differentation. While Arabidopsis has only one XND1 gene, the poplar genome contains four XND1-like genes. These genes are known as NAC118, NAC122, NAC128 and NAC129. We are in the process of determining the roles these four genes play in poplar growth and development. During this reporting period we completed our analysis of the four poplar XND1-like NACs and a manuscript describing our findings is in the final stages of preparation for submission. In complementary experiments, we engineered transgenic Arabidopsis plants to express high levels of NAC122 and NAC129. These transgenic poplar and Arabidopsis plants were evaluated at the whole plant, light microscope, and gene expression levels. We found that the poplar NAC genes prevent xylem formation and promote the expression of genes that protect plants from oxidative stress, suggesting that this family of NAC genes may repress xylem cell differentiation by repressing signaling networks that involve oxidative stress. We also completed a characterization of two protease genes, XCP1 and XCP2, that act downstream of the xylem NAC genes. Results of these efforts were presented orally to members of the Molecular Plant Sciences Graduate Program at Virginia Tech and as a published work in a peer-reviewed plant science journal. PARTICIPANTS: Eric Beers, PI, directed project, analyzed data, and wrote publications in collaboration with Amy Brunner, Department of Forestry, Virginia Tech. Dr. Brunner also provided training for graduate students in poplar tissue culture for the creation of transgenic poplar for high-level expression of transcription factors. During the current reporting period, six undergraduate students and two graduate students were trained in methods of poplar research. Two postdoctorals performed experiments required for characterizations of transcription factors associated with wood formation. One Master's student successfully defended his thesis on the topic of xylem differentiation. TARGET AUDIENCES: The principal target audience consisted of plant scientists studying wood formation. The secondary audience was undergraduate and graduate students and postdoctoral researchers being trained in poplar experimental biology. Finally, in the classroom with both undergraduate and graduate students, project results were used to illustrate fundamental concepts in plant biology and plant biotechnology. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
As a new model for plant cellulosic biomass production, poplar is an important component of future efforts to increase biofuels production. Advancing our knowledge in this area depends on increasing the numbers of graduate students and postdoctoral researchers trained in biomass research methods. During the current reporting period, two graduate students and three undergraduate students were trained in poplar gene expression analysis and genomics, and one postdoctoral researcher was trained in the use of poplar genomics resources and methods for identifying interacting proteins important to wood formation. Results for this period include a peer-reviewed publication documenting the intracellular dynamics of protease-dependent differentiation during wood formation.
Publications
- Avci, U., H.E. Petzold, I.O. Ismail, E.P. Beers, C.H. Haigler, 2008. Cysteine proteases XCP1 and XCP2 aid micro-autolysis within the intact central vacuole during xylogenesis in Arabidopsis roots. Plant J. 56: 303-315.
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Progress 10/01/07 to 09/30/08
Outputs
OUTPUTS: Transcription factors (TFs) are proteins that regulate gene expression. NAC domain (NAC) TFs comprise a large family of plant-specific TFs that regulate genes involved in many aspects of plant growth and development. Recent work by our lab and other labs in the U.S. and Japan has revealed that a small subset of these NACs are regulators of xylem differentiation. Xylem is the wood-forming tissue in plants. Understanding how plants produce wood is important to our ability to increase plant biomass and biofuels production. Some NACs promote xylem differentiation while others repress xylem differentiation. Our investigations focus on a subset of poplar NACs that are most closely related to the Arabidopsis gene XYLEM NAC DOMAIN1 (XND1), a gene shown by my lab to be able to repress xylem differentation. While Arabidopsis has only one XND1 gene, the poplar genome contains four XND1-like genes. These genes are known as Poptr118, Poptr122, Poptr128 and Poptr129. We are in the process of determining the roles these four genes play in poplar growth and development. During this reporting period we analyzed the expression patterns exhibited by the four poplar XND1-like NACs. Expression of all four genes was quantitatively evaluated at the organ level in primary and secondary (woody) stems as well as in roots, leaves and buds. Secondary stems were further divided into xylem, phloem and outer bark for additional measurements of gene expression at the tissue level. Changes in gene expression induced in so-called reaction wood--a type of wood that forms in response to branch bending--were also evaluated for all four genes. We also evaluated the effect of XND1 on wood formation in transgenic poplar plants engineered to express high levels of XND1. In complementary experiments, we engineered transgenic Arabidopsis plants to express high levels Poptr122 and Poptr129. These transgenic poplar and Arabidopsis plants were evaluated at the whole plant, light microscope, and gene expression levels. All of these experiments were conducted by graduate students and postdoctorals as part of their training. Results from these experiments were presentation to: 1) members of an undergraduate biotechnology club at James Madison University, Harrisonburg, VA, October 9, 2007, 2) an audience of genomics researchers at the 2008 Plant and Animal Genome Conference, San Diego, CA, January 10-12, 2008, and 3) members of the Molecular Plant Sciences Graduate Program during graduate student orientation week at Virginia Tech, Blacksburg, VA, August 19, 2008. PARTICIPANTS: Eric Beers, PI, directed project, analyzed data, and wrote publications in collaboration with Amy Brunner, Department of Forestry, Virginia Tech. Dr. Brunner also provided training for graduate students in poplar tissue culture for the creation of transgenic poplar for high-level expression of transcription factors. During the current reporting period, one undergraduate student and two graduate students were trained in methods of poplar research. Two postdoctorals performed experiments required for characterizations of transcription factors associated with wood formation. One postdoctoral was promoted to research scientist based on his contributions to the project. TARGET AUDIENCES: The principal target audience consisted of plant scientists studying the differentiation of vascular tissues and in particular the formation of wood (xylem). The secondary audience was undergraduate and graduate students and postdoctoral researchers being trained in poplar experimental biology. Finally, in the classroom with both undergraduate and graduate students, project results were used to illustrate fundamental concepts in plant biology and plant biotechnology. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
As a new model for plant cellulosic biomass production, poplar is an important component of future efforts to increase biofuels production. Advancing our knowledge in this area depends on increasing the numbers of graduate students and postdoctoral researchers trained in biomass research methods. During the current reporting period, two graduate students and one undergraduate were trained in poplar gene expression analysis and genomics, and one postdoctoral researcher was trained in the use of poplar genomics resources and methods for identifying interacting proteins important to wood formation. Results of selected gene expression experiments conducted during this period have been compiled in a book chapter that reviews currently available information about transcription factors that regulate wood formation in poplar.
Publications
- Zhao, C., Avci, U., Grant, E.H., Haigler, C.H. and Beers, E.P. (2008) XND1, a member of the NAC domain family in Arabidopsis thaliana, negatively regulates lignocellulose production and programmed cell death in xylem. Plant J. 53:425-436.
- Brunner, A.M. and Beers E.P. (2008). Transcription factors in poplar growth and development. In Poplar. Eds. C.P. Joshi and S. DiFazio. In the series: Genomics of Industrial Crop Plants, Series Ed. C. Kole. Science Publishers, Enfield, New Hampshire. In press.
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Progress 10/01/06 to 09/30/07
Outputs
OUTPUTS: Previous work by our lab and others has revealed that NAC domain transcription factors (NACs) are important regulators of xylem (wood) formation in Arabidopsis. This project involves translational research that will use information obtained from previous work with Arabidopsis to explore the role of NACs in wood formation in the model biomass crop, poplar. For this period, outputs included completion of analysis of expression of NAC domain transcription factors in poplar xylem and production of several lines of transgenic poplar and Arabidopsis plants overexpressing NACs or expressing dominant negative versions of NACs designed to block activity of endogenous NACs expressed in poplar wood.
PARTICIPANTS: Eric Beers, PI, directed project, analyzed data, and wrote publications. During the course of the project, one undergraduate student, one graduate student and one postdoctoral were trained in methods of poplar research.
TARGET AUDIENCES: The principal target audience consisted of plant scientists studying the differentiation of vascular tissues and in particular the formation of wood (xylem). The secondary audience was undergraduate and graduate students and postdoctoral researchers being trained in poplar experimental biology. Finally, in the classroom with both undergraduate and graduate students, project results were used to illustrate fundamental concepts in plant biology and plant biotechnology.
Impacts
As an emerging biomass model, significant progress in poplar research will depend on increases in numbers of graduate students and postdoctoral researchers trained in poplar research methods. During the current reporting period, one graduate student was trained in poplar genomics, tissue culture and transformation and one undergraduate student and one postdoctoral researcher were trained in the use of poplar genomics resources. Results were published describing the activity of a NAC domain transcription factor that can act as an inhibitor of wood synthesis in plants. This published work represents a novel perspective for researchers working with genes regulating wood formation, as virtually all prior work focused on genes that promote wood formation. The discovery of methods to prevent woody tissue formation will aid efforts to modify the nutritional quality of forage and fruit crops.
Publications
- Zhao, C., Avci, U., Grant, E.H., Haigler, C.H. and Beers, E.P. (2007) XND1, a member of the NAC domain family in Arabidopsis thaliana, negatively regulates lignocellulose production and programmed cell death in xylem. Plant Journal, doi: 10.1111/j.1365-313X.2007.03350.x. (in press).
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