WAGNER LAB PARTICIPATED IN BIOL425 CLASS

This semester Run Jin was a TA for Dr. John Wagner’s investigative biology class where open-ended, interesting biological problems are explored using modern lab techniques. Topics may include protein structure/function studies; genetic screens, genomics and gene expression studies; proteomics and protein purification techniques; and molecular cloning and DNA manipulation. Dr. Doris Wagner is a collaborator for the topic of this semester’s class which used Y2H NGS to identify interactors of a transcriptional adaptor protein. Sammy Klasfeld volunteered her computational skills to help students with gene expression data analysis. The course emphasizes developing scientific communication and independent research skills. Course topics reflect the interests of the Wagner lab.

TUG OF WAR: ADDING AND REMOVING HISTONE LYSINE METHYLATION IN ARABIDOPSIS

Citation:

Xiao, J, Lee US, Wagner D.  2016.  Tug of war: adding and removing histone lysine methylation in Arabidopsis, Sep 7. Curr Opin Plant Biol. 34:41-53.


Abstract:

Histone lysine methylation plays a fundamental role in the epigenetic regulation of gene expression in multicellular eukaryotes, including plants. It shapes plant developmental and growth programs as well as responses to the environment. The methylation status of certain amino-acids, in particular of the histone 3 (H3) lysine tails, is dynamically controlled by opposite acting histone methyltransferase ‘writers’ and histone demethylase ‘erasers’. The methylation status is interpreted by a third set of proteins, the histone modification ‘readers’, which specifically bind to a methylated amino-acid on the H3 tail. Histone methylation writers, readers, and erasers themselves are regulated by intrinsic or extrinsic stimuli; this forms a feedback loop that contributes to development and environmental adaptation in Arabidopsis and other plants. Recent studies have expanded our knowledge regarding the biological roles and dynamic regulation of histone methylation. In this review, we will discuss recent advances in understanding the regulation and roles of histone methylation in plants and animals.

Notes:

Xiao, JunLee, Un-SaWagner, DorisENGREVIEW2016/09/11 06:00Curr Opin Plant Biol. 2016 Sep 7;34:41-53. doi: 10.1016/j.pbi.2016.08.002.

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Making Flowers at the Right Time

Citation:

Wagner, D.  2016.  Making Flowers at the Right Time, May 9. Dev Cell. 37:208-10., Number 3

Abstract:

Different plant species flower in different seasons, but there is also annual variability depending on environmental conditions. In this issue of Developmental Cell, Hyun et al. (2016) show that Arabidopsis plants can flower without proper seasonal cues if they have developed past the juvenile phase and have high levels of gibberellin.

Notes:

Wagner, Doriseng2016/05/12 06:00Dev Cell. 2016 May 9;37(3):208-10. doi: 10.1016/j.devcel.2016.04.021.

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TRANSCRIPTIONAL RESPONSES TO THE AUXIN HORMONE

Citation:

Weijers, D, Wagner D.  2016.  Transcriptional Responses to the Auxin Hormone, Apr 29. Annu Rev Plant Biol. 67:539-74.

Abstract:

Auxin is arguably the most important signaling molecule in plants, and the last few decades have seen remarkable breakthroughs in understanding its production, transport, and perception. Recent investigations have focused on transcriptional responses to auxin, providing novel insight into the functions of the domains of key transcription regulators in responses to the hormonal cue and prominently implicating chromatin regulation in these responses. In addition, studies are beginning to identify direct targets of the auxin-responsive transcription factors that underlie auxin modulation of development. Mechanisms to tune the response to different auxin levels are emerging, as are first insights into how this single hormone can trigger diverse responses. Key unanswered questions center on the mechanism for auxin-directed transcriptional repression and the identity of additional determinants of auxin response specificity. Much of what has been learned in model plants holds true in other species, including the earliest land plants.

Notes:

Weijers, DolfWagner, Doriseng2016/02/26 06:00Annu Rev Plant Biol. 2016 Apr 29;67:539-74. doi: 10.1146/annurev-arplant-043015-112122. Epub 2016 Feb 22.

 

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50 YEARS OF ARABIDOPSIS RESEARCH: HIGHLIGHTS AND FUTURE DIRECTIONS

Citation:

Provart, NJ, Alonso J, Assmann SM, Bergmann D, Brady SM, Brkljacic J, Browse J, Chapple C, Colot V, Cutler S, Dangl J, Ehrhardt D, Friesner JD, Frommer WB, Grotewold E, Meyerowitz E, Nemhauser J, Nordborg M, Pikaard C, Shanklin J, Somerville C, Stitt M, Torii KU, Waese J, Wagner D, McCourt P.  2016. 50 years of Arabidopsis research: highlights and future directions. New Phytologist, 209(3), 921-944.

Abstract:

I. II. III. IV. V. VI. VII. VIII. IX. X. XI. XII. XIII. Natural variation and genome-wide association studies XIV. XV. XVI. XVII. References SUMMARY: The year 2014 marked the 25th International Conference on Arabidopsis Research. In the 50 yr since the first International Conference on Arabidopsis Research, held in 1965 in Gottingen, Germany, > 54 000 papers that mention Arabidopsis thaliana in the title, abstract or keywords have been published. We present herein a citational network analysis of these papers, and touch on some of the important discoveries in plant biology that have been made in this powerful model system, and highlight how these discoveries have then had an impact in crop species. We also look to the future, highlighting some outstanding questions that can be readily addressed in Arabidopsis. Topics that are discussed include Arabidopsis reverse genetic resources, stock centers, databases and online tools, cell biology, development, hormones, plant immunity, signaling in response to abiotic stress, transporters, biosynthesis of cells walls and macromolecules such as starch and lipids, epigenetics and epigenomics, genome-wide association studies and natural variation, gene regulatory networks, modeling and systems biology, and synthetic biology.

Notes:

Provart, Nicholas JAlonso, JoseAssmann, Sarah MBergmann, DominiqueBrady, Siobhan MBrkljacic, JelenaBrowse, JohnChapple, ClintColot, VincentCutler, SeanDangl, JeffEhrhardt, DavidFriesner, Joanna DFrommer, Wolf BGrotewold, ErichMeyerowitz, ElliotNemhauser, JenniferNordborg, MagnusPikaard, CraigShanklin, JohnSomerville, ChrisStitt, MarkTorii, Keiko UWaese, JamieWagner, DorisMcCourt, PeterENGREVIEW2015/10/16 06:00New Phytol. 2015 Oct 14. doi: 10.1111/nph.13687.

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AINTEGUMENTA AND AINTEGUMENTA-LIKE6/PLETHORA3 INDUCE LEAFY EXPRESSION IN RESPONSE TO AUXIN TO PROMOTE THE ONSET OF FLOWER FORMATION IN ARABIDOPSIS

Citation:

Yamaguchi, N, Jeong CW, Nole-Wilson S, Krizek BA, Wagner D.  2016.  AINTEGUMENTA and AINTEGUMENTA-LIKE6/PLETHORA3 Induce LEAFY Expression in Response to Auxin to Promote the Onset of Flower Formation in Arabidopsis, Jan. Plant Physiol. 170:283-93., Number 1

Abstract:

Proper timing of the onset to flower formation is critical for reproductive success. Monocarpic plants like Arabidopsis (Arabidopsis thaliana) switch from production of branches in the axils of leaves to that of flowers once in their lifecycle, during the meristem identity transition. The plant-specific transcription factor LEAFY (LFY) is necessary and sufficient for this transition. Previously, we reported that the plant hormone auxin induces LFY expression through AUXIN RESPONSE FACTOR5/MONOPTEROS (ARF5/MP). It is not known whether MP is solely responsible for auxin-directed transcriptional activation of LFY. Here, we show that two transcription factors belonging to the AINTEGUMENTA-LIKE/PLETHORA family, AINTEGUMENTA (ANT) and AINTEGUMENTA-LIKE6/PLETHORA3 (AIL6/PLT3), act in parallel with MP to upregulate LFY in response to auxin. ant ail6 mutants display a delay in the meristem identity transition and in LFY induction. ANT and AIL6/PLT3 are expressed prior to LFY and bind to the LFY promoter to control LFY mRNA accumulation. Genetic and promoter/reporter studies suggest that ANT/AIL6 act in parallel with MP to promote LFY induction in response to auxin sensing. Our study highlights the importance of two separate auxin-controlled pathways in the meristem identity transition.

Notes:

Yamaguchi, NobutoshiJeong, Cheol WoongNole-Wilson, StaciKrizek, Beth AWagner, DorisengResearch Support, Non-U.S. Gov’tResearch Support, U.S. Gov’t, Non-P.H.S.2015/11/06 06:00Plant Physiol. 2016 Jan;170(1):283-93. doi: 10.1104/pp.15.00969. Epub 2015 Nov 4.

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A DIRECT LINK BETWEEN ABSCISIC ACID SENSING AND THE CHROMATIN REMODELING ATPASE BRAHMA VIA CORE ABA SIGNALING PATHWAY COMPONENTS

Citation:

Peirats-Llobet, M. , Han, S-K, Jeong CW, Gonzalez-Guzman, M, Rodriguez, L, Belda-Palazon, B, Wagner, D and Rodriguez, PL. (2016) A direct link between abscisic acid sensing and the chromatin remodeling ATPase BRAHMA via core ABA signaling pathway components, Molecular Plant 9 (1):136-47.

Abstract:

Optimal response to drought is critical for plant survival and will impact biodiversity and crop performance during climate change. Mitotically heritable epigenetic or dynamic chromatin state changes have been implicated in the plant response to the drought stress hormone abscisic acid (ABA). The Arabidopsis SWI/SNF chromatin remodeling ATPase BRAHMA (BRM) modulates response to ABA by preventing premature activation of stress response pathways during germination. We show that core ABA signaling pathway components physically interact with BRM and posttranslationally modify BRM by phospho-/dephosphorylation. Genetic evidence suggests that BRM acts downstream of SnRK2.2/2.3 kinases and biochemical studies identified phosphorylation sites in the C-terminal region of BRM at SnRK2 target sites that are evolutionarily conserved. Finally, the phosphomimetic BRMS1760D S1762D mutant displays ABA hypersensitivity. Prior studies showed that BRM resides at target loci in the ABA pathway in the presence and absence of the stimulus, but is only active in the absence of ABA. Our data suggest that SnRK2-dependent phosphorylation of BRM leads to its inhibition and PP2CA-mediated dephosphorylation of BRM restores ability of BRM to repress ABA response. The findings point to the presence of a rapid phosphorylation-based switch to control BRM activity; this property could be potentially harnessed to improve drought tolerance in plants.

Notes:

Peirats-Llobet, MartaHan, Soon-KiGonzalez-Guzman, MiguelJeong, Cheol WoongRodriguez, LesiaBelda-Palazon, BorjaWagner, DorisRodriguez, Pedro LENG2015/10/27 06:00Mol Plant. 2015 Oct 21. pii: S1674-2052(15)00398-6. doi: 10.1016/j.molp.2015.10.003.

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