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The Arabidopsis lyrata genome sequence and the basis of rapid genome size change

Description: In our manuscript, we present a high-quality genome sequence of the Arabidopsis thaliana relative, Arabidopsis lyrata, produced by dideoxy sequencing. We have performed the usual types of genome analysis (gene annotation, dN/dS studies etc. etc.), but this is relegated to the Supporting Information. Instead, we focus on what was a major motivation for sequencing this genome, namely to understand how A. thaliana lost half its genome in a few million years and lived to tell the tale. The rather surprising conclusion is that there is not a single genomic feature that accounts for the reduced genome, but that every aspect centromeres, intergenic regions, transposable elements, gene family number is affected through hundreds of thousands of cuts. This strongly suggests that overall genome size in itself is what has been under selection, a suggestion that is strongly supported by our demonstration (using population genetics data from A. thaliana) that new deletions seem to be driven to fixation.
Date: April 29, 2011
Creator: Hu, Tina T.; Pattyn, Pedro; Bakker, Erica G.; Cao, Jun; Cheng, Jan-Fang; Clark, Richard M. et al.
Partner: UNT Libraries Government Documents Department

Summary of the International Conference on Arabidopsis Research 2011, June 22-25, 2011

Description: This project provided participant support for the gathering of plant biologists at the International Conferences on Arabidopsis Research (ICAR) in 2011. Arabidopsis thaliana, the reference flowering plant, has been intensely studied over the last 20 years and has proven to be an ideal model for studying nearly all aspects of plant biology. The success of this research field has been greatly facilitated by the openness and collegiality of the community fostered through multiple international forums including the ICAR. Advances in basic and applied plant biology are featured at the meeting, which is the primary gathering point for this strongly integrated international community. The ICAR convenes plant researchers, allows discussion and dissemination of the latest research in plant biology, and facilitates dialog among those that may be separated by geography, career stage, and culture. This project focused on facilitating access by early career scientists that have reduced access to attend major meetings.
Date: July 15, 2012
Creator: Meyers, Blake C
Partner: UNT Libraries Government Documents Department

Studies on Plant-aphid Interactions: a Novel Role for Trehalose Metabolism in Arabidopsis Defense Against Green Peach Aphid

Description: Myzus persicae (Sülzer), commonly known as the green peach aphid (GPA), is a polyphagous insect that can infest over 100 families of economically important plants and is major pest for vegetable crops. This study utilizes the Arabidopsis-GPA model system with the aim to elucidate the role of the plant disaccharide trehalose in providing defense against GPA. This study demonstrates a novel role for TPS11 in providing defense against GPA. TPS11 expression was found to be transiently induced in Arabidopsis plants in response to GPA infestation and the TPS11 gene was required for curtailing GPA infestation. TPS11, which encodes for trehalose phosphate synthase and phosphatase activities, contributes to the transient increase in trehalose in the GPA infested tissues. This work suggests that TPS11-dependent trehalose has a signaling function in plant defense against GPA. in addition, trehalose also has a more direct role in curtailing GPA infestation on Arabidopsis. This work also shows that TPS11 is able to modulate both carbohydrate metabolism and plant defenses in response to GPA infestation. the expression of PAD4, an Arabidopsis gene required for phloem-based defenses against GPA, was found to be delayed in GPA infested tps11 mutant plants along with increased sucrose levels and lower starch levels as compared to the GPA infested wild type plants. This work provides clear evidence that starch metabolism in Arabidopsis is altered in response to GPA feeding and that TPS11-modulated increase in starch contributes to the curtailment of GPA infestation in Arabidopsis.
Date: May 2012
Creator: Singh, Vijay
Partner: UNT Libraries

Final Report [Function of the Arabidopsis TIR1 gene in auxin response]

Description: During this grant period substantial progress was made in the characterization of the TIR1 gene in Arabidopsis. Studies showed that the TIR1 protein is part of a protein complex that includes AtCUL1, ASK1 and RBX1. This complex, called SCF-TIR1, functions in the ubiquitin-mediated protein degradation pathway. Our work is the first report of an SCF complex in a plant system. The results of our studies are described in more detail in the report together with a publication resulting from this study.
Date: December 18, 2000
Creator: Estelle, Mark
Partner: UNT Libraries Government Documents Department

N-Acylethanolamine (NAE) Profiles Change During Arabidopsis Thaliana Seed Germination and Seedling Growth

Description: An understanding of the potential roles as lipid mediators of a family of bioactive metabolites called N-acylethanolamines (NAEs) depends on their accurate identification and quantification. The levels of 18C unsaturated NAEs (e.g. NAE18:2, NAE 18:3, etc.) in wild-type seeds (about 2000 ng/g fw) generally decreased by about 80% during germination and post-germinative growth. In addition, results suggest NAE-degradative fatty acid amide hydrolase (FAAH) expression does not play a major role in normal NAE metabolism as previously thought. Seedlings germinated and grown in the presence of abscisic acid (ABA), an endogenous plant hormone, exhibited growth arrest and secondary dormancy, similar to the treatment of seedlings with exogenous N­lauroylethanolamine (NAE12:0). ABA-mediated growth arrest was associated with higher levels of unsaturated NAEs. Overall, these results are consistent with the concept that NAE metabolism is activated during seed germination and suggest that the reduction in unsaturated NAE levels is under strict temporal control and may be a requirement for normal seed germination and post-germinative growth.
Date: August 2006
Creator: Wiant, William C.
Partner: UNT Libraries

Regulatory elements of the floral homeotic gene AGAMOUS identified by phylogenetic footprinting and shadowing.

Description: OAK-B135 In Arabidopsis thaliana, cis-regulatory sequences of the floral homeotic gene AGAMOUS (AG) are located in the second intron. This 3 kb intron contains binding sites for two direct activators of AG, LEAFY (LFY) and WUSCHEL (WUS), along with other putative regulatory elements. We have used phylogenetic footprinting and the related technique of phylogenetic shadowing to identify putative cis-regulatory elements in this intron. Among 29 Brassicaceae, several other motifs, but not the LFY and WUS binding sites previously identified, are largely invariant. Using reporter gene analyses, we tested six of these motifs and found that they are all functionally important for activity of AG regulatory sequences in A. thaliana. Although there is little obvious sequence similarity outside the Brassicaceae, the intron from cucumber AG has at least partial activity in A. thaliana. Our studies underscore the value of the comparative approach as a tool that complements gene-by-gene promoter dissection, but also highlight that sequence-based studies alone are insufficient for a complete identification of cis-regulatory sites.
Date: June 1, 2003
Creator: Hong, R. L., Hamaguchi, L., Busch, M. A., and Weigel, D.
Partner: UNT Libraries Government Documents Department

Interaction of LEAFY, AGAMOUS, and TERMINAL FLOWER1 in maintaining floral identity in Arabidopsis

Description: OAK-B135 The Arabidopsis transcription factor LEAFY (LFY) acts upstream of homeotic genes such as AGAMOUS (AG) to confer floral identity on meristems that arise after the transition to reproductive development. Compared to the genetic circuitry regulating the establishment of floral meristem identity, little is known about its maintenance. Previous experiments with fly heterozygous plants and ag mutants grown in conditions that reduce the floral inductive stimulus have shown that both genes are required to prevent reversion of floral to inflorescence meristems. Here, we present evidence that LFY maintains floral meristem identity independently of AG, and that the primary role of LFY is either direct repression of shoot identity genes or repression of an intermediate factor that activates shoot identity genes. The latter conclusions were deduced from the phenotypes conferred by a gain-of-function transgene, LFY:VP16, that appears to act as a dominant negative, or antimorphic, allele during maintenance of floral meristem identity. These observations contrast with previous findings that LFY acts as a direct activator of floral homeotic genes, supporting the hypothesis that the transcriptional activity of LFY is dependent on specific co-regulators.
Date: February 22, 2002
Creator: Parcy, F., Bomblies, K., and Weigel, D.
Partner: UNT Libraries Government Documents Department

A chemical genetic screen uncovers a small molecule enhancer of the N-acylethanolamine degrading enzyme, fatty acid amide hydrolase, in Arabidopsis

Description: This article demonstrates the feasibility of using an unbiased chemical genetic approach to identify new pharmacological tools for manipulating FAAH- and NAE-mediated physiological processes in plants.
Date: January 23, 2017
Creator: Khan, Bibi Rafeiza; Faure, Lionel; Chapman, Kent D. & Blancaflor, Elison B.
Partner: UNT College of Arts and Sciences

Ultra-fast alterations in mRNA levels uncover multiple players in light stress acclimation in plants

Description: This article contains RNA sequencing analysis of Arabidopsis thaliana plants subjected to light stress in order to identify and characterize rapid changes in the steady-state level of different transcripts in response to light stress.
Date: September 26, 2015
Creator: Suzuki, Nobuhiro; Devireddy, Amith R.; Inupakutika, Madhuri A.; Baxter, Aaron; Miller, Gad; Song, Luhua et al.
Partner: UNT College of Arts and Sciences

Alterations in Fatty Acid Amide Hydrolase (Faah) Transcript Levels and Activity Lead to Changes in the Abiotic Stress Susceptibility of Arabidopsis Thaliana

Description: N-Acylethanolamines (NAEs) are a class of bioactive lipids, and FAAH is one of the enzymes responsible for degrading NAEs in both plants and animals. in plants, FAAH appears to be closely associated with ABA, a phytohormone which has long been associated with plant stress responses, since the overexpression of FAAH in Arabidopsis results in ABA hypersensitivity. Therefore, it is reasonable to speculate that alterations in FAAH transcript levels will result in altered stress responses in plants. to investigate this hypothesis experiments were carried out in which wild type (WT), FAAH-overexpressing (OE), and T-DNA insertional FAAH knockouts of Arabidopsis (faah) were grown in MS media under stress conditions. the stress conditions tested included chilling stress, heavy metal stress induced by cadmium or copper, nutrient limitations induced by low phosphorus or low nitrogen, salt stress induced with NaCl, and osmotic stress induced with mannitol. the OE plants were consistently hypersensitive to all stress conditions in relation to wild type plants. Inactive FAAH overexpressors did not have the hypersensitivity to the salt and osmotic stress of the active OE plants and were instead tolerant to these stresses. FAAH2 (faah2) knockouts and FAAH 1 and 2 double knockouts (faah 1+2) were based on some root development parameters somewhat more tolerant than WT plants, but more sensitive in terms of shoot growth. Collectively the data suggests that FAAH activity may interact with stress-responsive pathways in plants, perhaps including pathways involving ABA.
Date: May 2012
Creator: Gonzalez, Gabriel
Partner: UNT Libraries

Elemental Concentrations in the Seed of Mutants and Natural Variants of Arabidopsis thaliana Grown under Varying Soil Conditions

Description: Article on elemental concentrations in the seed of mutants and natural variants of Arabidopsis thaliana grown under varying soil conditions.
Date: May 2013
Creator: McDowell, Stephen C.; Akmakjian, Garo; Sladek, Chris; Mendoza-Cózatl, David; Morrissey, Joe B.; Saini, Nick et al.
Partner: UNT College of Arts and Sciences

Final Report for Regulation of Embryonic Development in Higher Plants

Description: The overall goal of the project was to define the cellular processes that underlie embryo development in plants at a mechanistic level. Our studies focused on a critical transcriptional regulator, Arabidopsis LEAFY COTYLEDON (LEC1), that is necessary and sufficient to induce processes required for embryo development. Because LEC1 regulates lipid accumulation during the maturation phase of embryo development, information about LEC1 may be useful in designing approaches to enhance biofuel production in plants. During the tenure of this project, we determined the molecular mechanisms by which LEC1 acts as a transcription factor in embryos. We also identified genes directly regulated by LEC1 and showed that many of these genes are involved in maturation processes. This information has been useful in dissecting the gene regulatory networks controlling embryo development. Finally, LEC1 is a novel isoform of a transcription factor that is conserved among eukaryotes, and LEC1 is active primarily in seeds. Therefore, we determined that the LEC1-type transcription factors first appeared in lycophytes during land plant evolution. Together, this study provides basic information that has implications for biofuel production.
Date: October 22, 2013
Creator: Harada, John J.
Partner: UNT Libraries Government Documents Department

Summary of the 19th International Conference on Arabidopsis Research (July 23-27, 2008 in Montreal, Canada)

Description: The 19th International Conference on Arabidopsis Research was a successful meeting attended by 815 scientists from around the world including 322 from the United States, 146 attendees from Canada, 179 from Europe, 134 from Asia, and 34 from a combination of Australia, South America, Africa and the Middle East. The scientific program was of excellent quality featuring 64 talks, including 41 from invited speakers. The Keynote Lecture, delivered by Chris Somerville (Energy Biosciences Institute/UC Berkeley) was particularly relevant to US agriculture and energy research and was titled The Development of Cellulosic Biofuels. There were also 6 community-organized workshops featuring 30 additional talks on topics including Frontiers in Plant Systems Biology, Sources and strategies for Gene Structure, Gene Function, and Metabolic Pathway annotation at TAIR and AraCyc, Advanced Bioinformatic Resources for Arabidopsis, Laser Microtechniques and Applications with Arabidopsis, Plant Proteomics- Tools, Approaches, Standards and Breakthroughs in Studying the Proteome, and Phytohormone Biosynthesis and Signal Transduction. Conference organizers arranged a special seminar by Jim Collins (head of the Directorate of Biosciences at NSF) to provide a community discussion forum regarding the future of Arabidopsis research. Approximately 575 posters were presented in topic areas including, among others, Development, Signal Transduction, Cell Walls, Non-Arabidopsis Systems, and Interactions with Biotic and Abiotic Factors. All conference abstracts and the full program are posted at The Arabidopsis Information Resource (TAIR), a publicly-accessibly website (www.arabidopsis.org/news/abstracts.jsp.) A survey completed by approximately 40% of the meeting attendees showed high satisfaction with the quality of the presentations, meeting organization and the city of Montreal. The conference is the largest annual international Arabidopsis venue which allowed the exchange of information at the forefront of Arabidopsis research and facilitated the establishment of new, and the strengthening of old, collaborations and networks. In addition, the conference provides the site for the annual meetings of ...
Date: October 1, 2009
Creator: Schroeder, Julian I.
Partner: UNT Libraries Government Documents Department

Identification and Characterization of an Arabidopsis thaliana Mutant with Tolerance to N-lauroylethanolamine

Description: N-Acylethanolamines (NAEs) are fatty acid derivatives in plants that negatively influence seedling growth. N-Lauroylethanolamine (NAE 12:0), one type of NAE, inhibits root length, increases radial swelling of root tips and reduces root hair numbers in a dose dependent manner in Arabidopis thaliana L. (ecotype Columbia). A forward genetics approach was employed by screening a population of T-DNA “activation-tagged” developed by the Salk Institute lines for NAE resistance to identify potential genes involved in NAE signaling events in Arabidopsis thaliana L. (ecotype Columbia). Seeds of the activation tagged lines were grown at 0, 25, 30, 50, 75 and 100 µM N-lauroylethanolamime (NAE 12:0). Ten plants which displayed NAE tolerance (NRA) seedling phenotypes, compared with wildtype (Columbia, Col-0) seedlings were identified. I focused on one mutant line, identified as NRA 25, where the tolerance to NAE 12:0 appears to be mediated by a single dominant, nuclear gene. Thermal asymmetric interlaced (TAIL) PCR identified the location of the T-DNA insert as 3.86 kbp upstream of the locus At1g68510. Quantitative PCR indicated that the transcript level corresponding to At1g68510 is upregulated approximately 20 fold in the mutant relative to wildtype. To determine whether the NAE tolerance in NRA 25 is associated with overexpression of At1g68510 I created overexpressing lines of At1g68510 with and without GFP fusions behind the 2X35S CaMV promoter. As predicted, results with overexpressing lines of At1g68510 also exhibited enhanced resistance to NAE when compared with the wildtype. Confocal images of the fusion proteins suggest that GFP-At1g68510 is concentrated in the nucleus and this was confirmed by counterstaining with 4', 6-Diamidino-2-phenylindol (DAPI). Futhermore, At1g68510 overexpressing lines and NRA 25 line also exhibited tolerance to abscisic acid (ABA) during seedling germination. The findings suggests that At1g68510 overexpression mediates seedling tolerance to both ABA and NAE, a mechanism independent of fatty acid amide hydrolase ...
Date: December 2015
Creator: Adhikari, Bikash
Partner: UNT Libraries

Interactions of N-Acylethanolamine Metabolism and Abscisic Acid Signaling in Arabidopsis Thaliana Seedlings

Description: N-Acylethanolamines (NAEs) are endogenous plant lipids hydrolyzed by fatty acid amide hydrolase (FAAH). When wildtype Arabidopsis thaliana seeds were germinated and grown in exogenous NAE 12:0 (35 µM and above), growth was severely reduced in a concentration dependent manner. Wildtype A. thaliana seeds sown on exogenous abscisic acid (ABA) exhibited similar growth reduction to that seen with NAE treatment. AtFAAH knockouts grew and developed similarly to WT, but AtFAAH overexpressor lines show markedly enhanced sensitivity to ABA. When low levels of NAE and ABA, which have very little effect on growth alone, were combined, there was a dramatic reduction in seedling growth in all three genotypes, indicating a synergistic interaction between ABA and NAE. Notably, this synergistic arrest of seedling growth was partially reversed in the ABA insensitive (abi) mutant abi3-1, indicating that a functional ABA signaling pathway is required for the full synergistic effect. This synergistic growth arrest results in an increased accumulation of NAEs, but no concomitant increase in ABA levels. The combined NAE and ABA treatment induced a dose-dependent increase in ABI3 transcript levels, which was inversely related to growth. The ABA responsive genes AtHVA22B and RD29B also had increased expression in both NAE and ABA treatment. The abi3-1 mutant showed no expression of ABI3 and AtHVA22B, but RD29B expression remained similar to wildtype seedlings, suggesting an alternate mechanism for NAE and ABA interaction. Taken together, these data suggest that NAE metabolism acts through ABI3-dependent and independent pathways in the negative regulation of seedling development.
Date: August 2010
Creator: Cotter, Matthew Q.
Partner: UNT Libraries

Expression analysis of the fatty acid desaturase 2-4 and 2-3 genes from Gossypium hirsutum in transformed yeast cells and transgenic Arabidopsis plants.

Description: Fatty acid desaturase 2 (FAD2) enzymes are phosphatidylcholine desaturases occurring as integral membrane proteins in the endoplasmic reticulum membrane and convert monounsaturated oleic acid into polyunsaturated linoleic acid. The major objective of this research was to study the expression and function of two cotton FAD2 genes (the FAD2-3 and FAD2-4 genes) and their possible role in plant sensitivity to environmental stress, since plants may increase the polyunsaturated phospholipids in membranes under environmental stress events, such as low temperature and osmotic stress. Two FAD2 cDNA clones corresponding to the two FAD2 genes have been isolated from a cotton cDNA library, indicating both genes are truly expressed in cotton. Model yeast cells transformed with two cotton FAD2 genes were used to study the chilling sensitivity, ethanol tolerance, and growth rate of yeast cells. The expression patterns of the two FAD2 genes were analyzed by reverse transcription polymerase chain reactions (RT-PCR) and Western blot analyses in cotton plants under different treatment conditions. The coding regions of both FAD2 genes were inserted downstream from the CaMV 35S promoter in the pMDC gateway binary vector system. Five different FAD2/pMDC constructs were transformed into the Arabidopsis fad2 knockout mutant background, and multiple potential transgenic Arabidopsis plant lines harboring the cotton FAD2 genes were generated. The cotton FAD2 genes were amplified by the polymerase chain reaction (PCR) from the genomic DNAs isolated from the transgenic Arabidopsis T1 plant lines. Complementation of the putative transgenic Arabidopsis plants with the two cotton FAD2 genes was demonstrated by gas chromatography analyses of the fatty acid profiles of leaf tissues. The cellular localization of cotton FAD2-4 polypeptides with N-terminal green fluorescence protein (GFP) was visualized by confocal fluorescence microscopy. The phenotype of transgenic Arabidopsis plants transformed with the cotton FAD2-4 gene was compared to Arabidopsis knockout fad2 mutant plants and wild ...
Date: August 2008
Creator: Zhang, Daiyuan
Partner: UNT Libraries

Building beauty: the genetic control of floral patterning

Description: OAK-B135 Floral organ identity is controlled by combinatorial action of homeotic genes expressed in different territories within the emerging flower. This review discusses recent progress in our understanding of floral homeotic genes, with an emphasis on how their region-specific expression is regulated.
Date: February 1, 2002
Creator: Lohmann, J. U. & Weigel, D.
Partner: UNT Libraries Government Documents Department

STI. DE-FG02-00ER1505 [Brief summary of 11th International Conference on Arabidopsis Research]

Description: The 11th International Conference on Arabidopsis Research was held in Madison, Wisconsin, June 24 through June 28, 2000. Arabidopsis thaliana has been the subject of genetic study for many years. However, during the last decade, the number of research laboratories using Arabidopsis as a model system has increased tremendously, and Arabidopsis is currently being used to study all aspects of plant biology. The rapid rate of progress in Arabidopsis research, including the completion of the genomic sequence, underscores the usefulness of holding a meeting every year. These conferences provide an important opportunity for the Arabidopsis community to interact and exchange information. The meeting opened with an evening keynote address on the global impact of plant biology, delivered by Richard Jefferson, the Executive Director of CAMBIA (Center for the Application of Molecular Biology to International Agriculture). This was followed by short updates from each of the NSF-funded Plant Genome groups. Many of these groups are carrying out projects that impact the Arabidopsis community. Each of the 17 platform sessions consisted of talks from two invited speakers followed by two short talks that were chosen from the submitted poster abstracts. A concerted effort was made to invite junior investigators, including graduate students and postdocs, to give these talks. Posters were available for viewing during three formal sessions, and, because the poster session was adjacent to the lecture hall, it was easy for participants to go back and forth between posters and lectures. Finally, a mixer and an informal banquet provided opportunities for participants to meet new people and renew acquaintances. Furthermore, the registration package included all lunches and dinners together in a cafeteria next to the posters and lecture hall, thus encouraging the meeting of established investigators with students and postdocs. The North American Arabidopsis Steering Committee (elected by electronic ballot by ...
Date: June 24, 2000
Partner: UNT Libraries Government Documents Department

Progress Report for DOE DE-FG03-98ER20317 ''Regulation of the floral homeotic gene AGAMOUS'' Current and Final Funding Period: September 1, 2002, to December 31, 2002

Description: OAK-B135 Results obtained during this funding period: (1) Phylogenetic footprinting of AG regulatory sequences Sequences necessary and sufficient for AGAMOUS (AG) expression in the center of Arabidopsis flowers are located in the second intron, which is about 3 kb in size. This intron contains binding sites for two transcription factors, LEAFY (LFY) and WUSCHEL (WUS), which are direct activators of AG. We used the new method of phylogenetic shadowing to identify new regulatory elements. Among 29 Brassicaceae, several other motifs, but not the LFY and WUS binding sites previously identified, are largely invariant. Using reporter gene analyses, we tested six of these motifs and found that they are all functionally important for activity of AG regulatory sequences in A. thaliana. (2) Repression of AG by MADS box genes A candidate for repressing AG in the shoot apical meristem has been the MADS box gene FUL, since it is expressed in the shoot apical meristem and since an activated version (FUL:VP16) leads to ectopic AG expression in the shoot apical meristem. However, there is no ectopic AG expression in full single mutants. We therefore started to generate VP16 fusions of several other MADS box genes expressed in the shoot apical meristem, to determine which of these might be candidates for FUL redundant genes. We found that AGL6:VP16 has a similar phenotype as FUL:VP16, suggesting that AGL6 and FUL interact. We are now testing this hypothesis. (3) Two candidate AG regulators, WOW and ULA Because the phylogenetic footprinting project has identified several new candidate regulatory motifs, of which at least one (the CCAATCA motif) has rather strong effects, we had decided to put the analysis of WOW and ULA on hold, and to focus on using the newly identified motifs as tools. We conduct ed yeast one-hybrid screen with two of the ...
Date: March 11, 2003
Creator: Weigel, D.
Partner: UNT Libraries Government Documents Department

Role of a chalcone isomerase-like protein in flavonoid biosynthesis in Arabidopsis thaliana

Description: This article identifies two chil mutants with a seed colour similar to that of wild-type Arabidopsis, but in sharp contrast to the characteristic transparent testa seed phenotype associated with other known flavonoid pathway genes.
Date: August 13, 2015
Creator: Jiang, Wenbo; Yin, Qinggang; Wu, Ranran; Zheng, Guangshun; Liu, Jinyue; Dixon, R. A. et al.
Partner: UNT College of Arts and Sciences