@article{imkampe_halter_huang_schulze_mazzotta_schmidt_manstretta_postel_wierzba_yang_et al._2017, title={The Arabidopsis Leucine-Rich Repeat Receptor Kinase BIR3 Negatively Regulates BAK1 Receptor Complex Formation and Stabilizes BAK1}, volume={29}, ISSN={["1532-298X"]}, DOI={10.1105/tpc.17.00376}, abstractNote={The receptor kinase BIR3 negatively regulates cell surface receptor complexes and thereby prevents unwanted activation of immune and hormone responses. BAK1 is a coreceptor and positive regulator of multiple ligand binding leucine-rich repeat receptor kinases (LRR-RKs) and is involved in brassinosteroid (BR)-dependent growth and development, innate immunity, and cell death control. The BAK1-interacting LRR-RKs BIR2 and BIR3 were previously identified by proteomics analyses of in vivo BAK1 complexes. Here, we show that BAK1-related pathways such as innate immunity and cell death control are affected by BIR3 in Arabidopsis thaliana. BIR3 also has a strong negative impact on BR signaling. BIR3 directly interacts with the BR receptor BRI1 and other ligand binding receptors and negatively regulates BR signaling by competitive inhibition of BRI1. BIR3 is released from BAK1 and BRI1 after ligand exposure and directly affects the formation of BAK1 complexes with BRI1 or FLAGELLIN SENSING2. Double mutants of bak1 and bir3 show spontaneous cell death and constitutive activation of defense responses. BAK1 and its closest homolog BKK1 interact with and are stabilized by BIR3, suggesting that bak1 bir3 double mutants mimic the spontaneous cell death phenotype observed in bak1 bkk1 mutants via destabilization of BIR3 target proteins. Our results provide evidence for a negative regulatory mechanism for BAK1 receptor complexes in which BIR3 interacts with BAK1 and inhibits ligand binding receptors to prevent BAK1 receptor complex formation.}, number={9}, journal={PLANT CELL}, author={Imkampe, Julia and Halter, Thierry and Huang, Shuhua and Schulze, Sarina and Mazzotta, Sara and Schmidt, Nikola and Manstretta, Raffaele and Postel, Sandra and Wierzba, Micheal and Yang, Yong and et al.}, year={2017}, month={Sep}, pages={2285–2303} }
 @article{clouse_2016, title={Brassinosteroid/Abscisic Acid Antagonism in Balancing Growth and Stress}, volume={38}, ISSN={["1878-1551"]}, DOI={10.1016/j.devcel.2016.07.005}, abstractNote={In this issue of Developmental Cell, Gui et al., 2016Gui J. Zheng S. Liu C. Shen J. Li J. Li L. Dev. Cell. 2016; 38 (this issue): 201-213Google Scholar show that an abscisic acid-inducible remorin protein in rice directly interacts with critical brassinosteroid signaling components to attenuate the brassinosteroid response, thus illuminating one aspect of the brassinosteroid/abscisic acid antagonism. In this issue of Developmental Cell, Gui et al., 2016Gui J. Zheng S. Liu C. Shen J. Li J. Li L. Dev. Cell. 2016; 38 (this issue): 201-213Google Scholar show that an abscisic acid-inducible remorin protein in rice directly interacts with critical brassinosteroid signaling components to attenuate the brassinosteroid response, thus illuminating one aspect of the brassinosteroid/abscisic acid antagonism. Plant hormones regulate numerous aspects of plant growth, development, and environmental response through a diverse array of signal transduction pathways that modulate the expression of thousands of different genes required for cell elongation, division, and differentiation. Brassinosteroids (BRs), belonging to one such class of plant hormones, have structural similarity to mammalian steroid hormones and, like their animal counterparts, have a profound influence on cellular dynamics and function. Null mutations in genes encoding BR biosynthetic enzymes or signal transduction components show severe phenotypes including dwarfism, disruptions in leaf, flower, and root development, and altered vascular structure, suggesting that BRs are essential for normal plant development (Belkhadir and Jaillais, 2015Belkhadir Y. Jaillais Y. New Phytol. 2015; 206: 522-540Crossref PubMed Scopus (159) Google Scholar). In changing environmental conditions, plants must shift resources from growth and development to adaptation to stresses such as drought and temperature extremes. This process is accelerated by another plant hormone, abscisic acid (ABA), which responds to drought in part by regulating leaf stomatal aperture, although it also functions in embryo development and seed germination (Hauser et al., 2011Hauser F. Waadt R. Schroeder J.I. Curr. Biol. 2011; 21: R346-R355Abstract Full Text Full Text PDF PubMed Scopus (334) Google Scholar). As part of the adaptive response to stress, ABA can inhibit vegetative growth and thus oppose the growth-promoting properties of BRs. Twenty years ago it was found that mutants unresponsive to the inhibitory effect of BRs on root elongation were hypersensitive to root length inhibition by ABA, suggesting an antagonistic interaction between these two hormones (Clouse et al., 1996Clouse S.D. Langford M. McMorris T.C. Plant Physiol. 1996; 111: 671-678Crossref PubMed Scopus (630) Google Scholar). Numerous other examples of the BR/ABA antagonism have been reported since, but the precise molecular mechanisms that are responsible for this physiological response could not be uncovered until both BR and ABA signal transduction pathways became well characterized (Saini et al., 2015Saini S. Sharma I. Pati P.K. Front. Plant Sci. 2015; 6: 1-17Crossref Scopus (131) Google Scholar). Gui et al., 2016Gui J. Zheng S. Liu C. Shen J. Li J. Li L. Dev. Cell. 2016; 38 (this issue): 201-213Google Scholar now describe one mechanism of BR/ABA interaction involving a remorin protein that is regulated by ABA and in turn regulates BR signal transduction. BRs are perceived by the extracellular domain of a leucine-rich repeat receptor kinase named BRASSINOSTEROID INSENSITIVE 1 (BRI1), which, in the presence of ligand, interacts with and reciprocally transphosphorylates a co-receptor from the SOMATIC EMBRYOGENESIS RECEPTOR KINASE (SERK) family of smaller leucine-rich repeat receptor kinases (Figure 1). The formation of an active complex between BRI1 and SERK family members such as SERK1 and SERK3 (also known as BRI1-ASSOCIATED RECEPTOR KINASE 1 or BAK1) is a critical step in BR signaling because it initiates a phospho-relay involving cytoplasmic kinases and phosphatases that ultimately results in the activation of specific transcription factors that regulate the expression of nearly 1,000 genes (Belkhadir and Jaillais, 2015Belkhadir Y. Jaillais Y. New Phytol. 2015; 206: 522-540Crossref PubMed Scopus (159) Google Scholar). In both Arabidopsis thaliana and rice, BRI1 INHIBITIOR KINASE 1 (BKI1) is a membrane-bound negative regulator of BR signaling that binds to BRI1 in the absence of BR and prevents the interaction of BRI1 with SERK co-receptors. Upon BR binding to BRI1, BKI1 is phosphorylated on a tyrosine residue and released from the membrane, allowing the BRI1/SERK complex to form, which propagates BR signaling downstream (Jiang et al., 2015Jiang J. Wang T. Wu Z. Wang J. Zhang C. Wang H. Wang Z.X. Wang X. Mol. Plant. 2015; 8: 1675-1678Abstract Full Text Full Text PDF Scopus (33) Google Scholar). Gui et al., 2016Gui J. Zheng S. Liu C. Shen J. Li J. Li L. Dev. Cell. 2016; 38 (this issue): 201-213Google Scholar have now identified a protein that has a function similar to BKI1, i.e., disruption of the BRI1/SERK complex formation and downregulation of BR signaling, but with a twist: this rice protein, termed OsREM4.1, is encoded by a gene whose transcript levels are regulated by ABA. Specifically, OsREM4.1 levels are increased by elevated ABA levels through a bZIP transcription factor (OsbZIP23) in the ABA signal transduction pathway. In Arabidopsis, it is known that binding of ABA to its soluble receptor results in inactivation of a PP2C phosphatase, which in turn allows activation of a SnRK2 kinase that phosphorylates downstream transcription factors and ion channels required for the ABA response (Hauser et al., 2011Hauser F. Waadt R. Schroeder J.I. Curr. Biol. 2011; 21: R346-R355Abstract Full Text Full Text PDF PubMed Scopus (334) Google Scholar). Recently, it was also shown in rice that OsbZIP23 is phosphorylated by a SnRK2 kinase in response to ABA (Zong et al., 2016Zong W. Tang N. Yang J. Peng L. Ma S. Xu Y. Li G. Xiong L. Plant Physiol. 2016; (in press. Published online June 20, 2016)https://doi.org/10.1104/pp.16.00469Crossref Scopus (165) Google Scholar). OsREM4.1 belongs to the plant-specific remorin family of proteins whose members are membrane-associated and often involved in plant-microbe interactions or hormone response. After establishing that OsREM4.1 transcription was specifically upregulated by ABA, Gui et al., 2016Gui J. Zheng S. Liu C. Shen J. Li J. Li L. Dev. Cell. 2016; 38 (this issue): 201-213Google Scholar then searched for OsREM4.1-interacting proteins by immunoprecipitation followed by liquid chromatography/tandem mass spectrometry. A particularly interesting candidate uncovered was OsSERK1, the co-receptor of BRI1 in rice. Numerous independent lines of analysis confirmed the OsREM4.1/OsSERK1 interaction, and examination of the phenotype of transgenic lines expressing either high or low levels of OsREM4.1 showed that OsREM4.1 was a negative regulator of BR signaling. Moreover, OsREM4.1 binds to the activation loop of the OsSERK1 kinase domain, thereby inhibiting the formation of the OsSERK1/OsBRI1 complex and preventing transphosphorylation of BRI1 and SERK1, thus negatively regulating BR signaling. Interestingly, increased BR levels caused OsBRI1 to directly phosphorylate OsREM4.1 and release its inhibition of the OsSERK1/OsBRI1 active complex in a manner reminiscent of the BKI1 protein. When viewed together, the accumulated evidence of Gui et al., 2016Gui J. Zheng S. Liu C. Shen J. Li J. Li L. Dev. Cell. 2016; 38 (this issue): 201-213Google Scholar suggests a central role for OSREM4.1 in mediating the ABA/BR antagonism in rice. Under conditions of stress, ABA levels are rapidly elevated, increasing OsREM4.1 levels to facilitate disruption of the critical OsBRI1/OsSERK1 complex and downregulation of BR signaling, which would favor shifting plant resources from BR-promoted growth to ABA-regulated stress responses. When stress decreases, ABA levels fall and BR-promoted phosphorylation of OsREM4.1 by OsBRI1 increases, releasing OsREM4.1 from the complex and thus allowing transphosphorylation of OsBRI1/OsSERK1 to reactivate the growth-promoting BR signal transduction pathway (Figure 1). A recent study demonstrated direct interaction between downstream elements of the BR and ABA signaling pathways in Arabidopsis, providing another mechanism of antagonistic crosstalk in the regulation of root growth. BRASSINAZOLE RESISTANT 1 (BZR1), one of the primary transcription factors regulating BR-responsive genes (Figure 1), was found to directly bind to the promoter of ABSCISIC ACID INSENSTIVE 5 (ABI5), an important transcription factor in ABA signaling, leading to suppressed ABI5 expression and reduced ABA response (Yang et al., 2016Yang X. Bai Y. Shang J. Xin R. Tang W. Plant Cell Environ. 2016; (in press. Published online May 5, 2016)https://doi.org/10.1111/pce.12763Crossref Scopus (59) Google Scholar). Several other examples of direct interaction between BR and ABA signaling components in a variety of physiological processes have also been reported (Hu and Yu, 2014Hu Y. Yu D. Plant Cell. 2014; 26: 4394-4408Crossref PubMed Scopus (177) Google Scholar, Shang et al., 2016Shang Y. Dai C. Lee M.M. Kwak J.M. Nam K.H. Mol. Plant. 2016; 9: 447-460Abstract Full Text Full Text PDF PubMed Scopus (113) Google Scholar). The work of Gui et al. in this issue provides an addition to this growing list of mechanisms integrating distinct hormone signal transduction pathways that balance complex developmental programs leading to plant growth with those regulating adaptation to changing environments. This article was written while serving in a paid position at the National Science Foundation. Any opinions or conclusions expressed in this article are those of the author and do not necessarily reflect the views of the National Science Foundation. OsREM4.1 Interacts with OsSERK1 to Coordinate the Interlinking between Abscisic Acid and Brassinosteroid Signaling in RiceGui et al.Developmental CellJuly 14, 2016In BriefThe hormones abscisic acid (ABA) and brassinosteroid (BR) exhibit antagonistic interactions during plant development. Gui et al. now identify rice OsREM4.1 as a link between the ABA and BR signaling pathways. OsREM4.1, which is transcriptionally upregulated by ABA, inhibits the formation and activation of a BR receptor kinase (OsBRI1-OsSERK1) complex. Full-Text PDF Open Archive}, number={2}, journal={DEVELOPMENTAL CELL}, author={Clouse, Steven D.}, year={2016}, month={Jul}, pages={118–120} }
 @article{tunc-ozdemir_urano_jaiswal_clouse_jones_2016, title={Direct Modulation of Heterotrimeric G Protein-coupled Signaling by a Receptor Kinase Complex}, volume={291}, ISSN={["1083-351X"]}, DOI={10.1074/jbc.c116.736702}, abstractNote={Plants and some protists have heterotrimeric G protein complexes that activate spontaneously without canonical G protein-coupled receptors (GPCRs). In Arabidopsis, the sole 7-transmembrane regulator of G protein signaling 1 (AtRGS1) modulates the G protein complex by keeping it in the resting state (GDP-bound). However, it remains unknown how a myriad of biological responses is achieved with a single G protein modulator. We propose that in complete contrast to G protein activation in animals, plant leucine-rich repeat receptor-like kinases (LRR RLKs), not GPCRs, provide this discrimination through phosphorylation of AtRGS1 in a ligand-dependent manner. G protein signaling is directly activated by the pathogen-associated molecular pattern flagellin peptide 22 through its LRR RLK, FLS2, and co-receptor BAK1.}, number={27}, journal={JOURNAL OF BIOLOGICAL CHEMISTRY}, author={Tunc-Ozdemir, Meral and Urano, Daisuke and Jaiswal, Dinesh Kumar and Clouse, Steven D. and Jones, Alan M.}, year={2016}, month={Jul}, pages={13918–13925} }
 @misc{clouse_2015, title={A History of Brassinosteroid Research from 1970 through 2005: Thirty-Five Years of Phytochemistry, Physiology, Genes, and Mutants}, volume={34}, ISSN={["1435-8107"]}, DOI={10.1007/s00344-015-9540-7}, number={4}, journal={JOURNAL OF PLANT GROWTH REGULATION}, author={Clouse, Steven D.}, year={2015}, month={Dec}, pages={828–844} }
 @article{mitra_chen_dhandaydham_wang_blackburn_kota_goshe_schwartz_huber_clouse_2015, title={An autophosphorylation site database for leucine-rich repeat receptor-like kinases in Arabidopsis thaliana}, volume={82}, ISSN={["1365-313X"]}, DOI={10.1111/tpj.12863}, abstractNote={Summary}, number={6}, journal={PLANT JOURNAL}, author={Mitra, Srijeet K. and Chen, Ruiqiang and Dhandaydham, Murali and Wang, Xiaofeng and Blackburn, Robert Kevin and Kota, Uma and Goshe, Michael B. and Schwartz, Daniel and Huber, Steven C. and Clouse, Steven D.}, year={2015}, month={Jun}, pages={1042–1060} }
 @article{oh_wang_kim_wu_clouse_huber_2014, title={The Carboxy-terminus of BAK1 regulates kinase activity and is required for normal growth of Arabidopsis (Retracted article. See vol. 7, 960, 2016)}, volume={5}, ISSN={["1664-462X"]}, DOI={10.3389/fpls.2014.00016}, abstractNote={Binding of brassinolide to the brassinosteroid-insenstive 1(BRI1) receptor kinase promotes interaction with its co-receptor, BRI1-associated receptor kinase 1 (BAK1). Juxtaposition of the kinase domains that occurs then allows reciprocal transphosphorylation and activation of both kinases, but details of that process are not entirely clear. In the present study we show that the carboxy (C)-terminal polypeptide of BAK1 may play a role. First, we demonstrate that the C-terminal domain is a strong inhibitor of the transphosphorylation activity of the recombinant BAK1 cytoplasmic domain protein. However, recombinant BAK1 lacking the C-terminal domain is unable to transactivate the peptide kinase activity of BRI1 in vitro. Thus, the C-terminal domain may play both a positive and negative role. Interestingly, a synthetic peptide corresponding to the full C-terminal domain (residues 576–615 of BAK1) interacted with recombinant BRI1 in vitro, and that interaction was enhanced by phosphorylation at the Tyr-610 site. Expression of a BAK1 C-terminal domain truncation (designated BAK1-ΔCT-Flag) in transgenic Arabidopsis plants lacking endogenous bak1 and its functional paralog, bkk1, produced plants that were wild type in appearance but much smaller than plants expressing full-length BAK1-Flag. The reduction in growth may be attributed to a partial inhibition of BR signaling in vivo as reflected in root growth assays but other factors are likely involved as well. Our working model is that in vivo, the inhibitory action of the C-terminal domain of BAK1 is relieved by binding to BRI1. However, that interaction is not essential for BR signaling, but other aspects of cellular signaling are impacted when the C-terminal domain is truncated and result in inhibition of growth. These results increase the molecular understanding of the C-terminal domain of BAK1 as a regulator of kinase activity that may serve as a model for other receptor kinases.}, journal={FRONTIERS IN PLANT SCIENCE}, author={Oh, Man-Ho and Wang, Xuejun and Kim, Sang Yeol and Wu, Xia and Clouse, Steven D. and Huber, Steven C.}, year={2014}, month={Feb} }
 @article{halter_imkampe_mazzotta_wierzba_postel_buecherl_kiefer_stahl_chinchilla_wang_et al._2014, title={The Leucine-Rich Repeat Receptor Kinase BIR2 Is a Negative Regulator of BAK1 in Plant Immunity}, volume={24}, ISSN={["1879-0445"]}, DOI={10.1016/j.cub.2013.11.047}, abstractNote={BackgroundTransmembrane leucine-rich repeat (LRR) receptors are commonly used innate immune receptors in plants and animals but can also sense endogenous signals to regulate development. BAK1 is a plant LRR-receptor-like kinase (RLK) that interacts with several ligand-binding LRR-RLKs to positively regulate their functions. BAK1 is involved in brassinosteroid-dependent growth and development, innate immunity, and cell-death control by interacting with the brassinosteroid receptor BRI1, immune receptors, such as FLS2 and EFR, and the small receptor kinase BIR1, respectively.ResultsIdentification of in vivo BAK1 complex partners by LC/ESI-MS/MS uncovered two novel BAK1-interacting RLKs, BIR2 and BIR3. Phosphorylation studies revealed that BIR2 is unidirectionally phosphorylated by BAK1 and that the interaction between BAK1 and BIR2 is kinase-activity dependent. Functional analyses of bir2 mutants show differential impact on BAK1-regulated processes, such as hyperresponsiveness to pathogen-associated molecular patterns (PAMP), enhanced cell death, and resistance to bacterial pathogens, but have no effect on brassinosteroid-regulated growth. BIR2 interacts constitutively with BAK1, thereby preventing interaction with the ligand-binding LRR-RLK FLS2. PAMP perception leads to BIR2 release from the BAK1 complex and enables the recruitment of BAK1 into the FLS2 complex.ConclusionsOur results provide evidence for a new regulatory mechanism for innate immune receptors with BIR2 acting as a negative regulator of PAMP-triggered immunity by limiting BAK1-receptor complex formation in the absence of ligands.}, number={2}, journal={CURRENT BIOLOGY}, author={Halter, Thierry and Imkampe, Julia and Mazzotta, Sara and Wierzba, Michael and Postel, Sandra and Buecherl, Christoph and Kiefer, Christian and Stahl, Mark and Chinchilla, Delphine and Wang, Xiaofeng and et al.}, year={2014}, month={Jan}, pages={134–143} }
 @article{bajwa_wang_blackburn_goshe_mitra_williams_bishop_krasnyanski_allen_huber_et al._2013, title={Identification and Functional Analysis of Tomato BRI1 and BAK1 Receptor Kinase Phosphorylation Sites}, volume={163}, ISSN={["1532-2548"]}, DOI={10.1104/pp.113.221465}, abstractNote={Abstract}, number={1}, journal={PLANT PHYSIOLOGY}, author={Bajwa, Vikramjit S. and Wang, Xiaofeng and Blackburn, R. Kevin and Goshe, Michael B. and Mitra, Srijeet K. and Williams, Elisabeth L. and Bishop, Gerard J. and Krasnyanski, Sergei and Allen, George and Huber, Steven C. and et al.}, year={2013}, month={Sep}, pages={30–42} }
 @article{fabregas_li_boeren_nash_goshe_clouse_vries_cano-delgado_2013, title={The BRASSINOSTEROID INSENSITIVE1-LIKE3 Signalosome Complex Regulates Arabidopsis Root Development}, volume={25}, ISSN={["1532-298X"]}, DOI={10.1105/tpc.113.114462}, abstractNote={Abstract}, number={9}, journal={PLANT CELL}, author={Fabregas, Norma and Li, Na and Boeren, Sjef and Nash, Tara E. and Goshe, Michael B. and Clouse, Steven D. and Vries, Sacco and Cano-Delgado, Ana I.}, year={2013}, month={Sep}, pages={3377–3388} }
 @article{oh_wang_clouse_huber_2012, title={Deactivation of the Arabidopsis BRASSINOSTEROID INSENSITIVE 1 (BRI1) receptor kinase by autophosphorylation within the glycine-rich loop}, volume={109}, ISSN={["0027-8424"]}, DOI={10.1073/pnas.1108321109}, abstractNote={
            The activity of the dual-specificity receptor kinase, brassinosteroid insensitive 1 (BRI1), reflects the balance between phosphorylation-dependent activation and several potential mechanisms for deactivation of the receptor. In the present report, we elucidate a unique mechanism for deactivation that involves autophosphorylation of serine-891 in the ATP-binding domain. Serine-891 was identified previously as a potential site of autophosphorylation by mass spectrometry, and sequence-specific antibodies and mutagenesis studies now unambiguously establish phosphorylation of this residue. In vivo, phosphorylation of serine-891 increased slowly with time following application of brassinolide (BL) to
            Arabidopsis
            seedlings, whereas phosphorylation of threonine residues increased rapidly and then remained constant. Transgenic plants expressing the BRI1(S891A)–Flag-directed mutant have increased hypocotyl and petiole lengths, relative to wild-type BRI1–Flag (both in the
            bri1-5
            background), and accumulate higher levels of the unphosphorylated form of the BES1 transcription factor in response to exogenous BL. In contrast, plants expressing the phosphomimetic S891D-directed mutant are severely dwarfed and do not accumulate unphosphorylated BES1 in response to BL. Collectively, these results suggest that autophosphorylation of serine-891 is one of the deactivation mechanisms that inhibit BRI1 activity and BR signaling in vivo. Many arginine-aspartate (RD)-type leucine-rich repeat receptor-like kinases have a phosphorylatable residue within the ATP-binding domain, suggesting that this mechanism may play a broad role in receptor kinase deactivation.
          }, number={1}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Oh, Man-Ho and Wang, Xiaofeng and Clouse, Steven D. and Huber, Steven C.}, year={2012}, month={Jan}, pages={327–332} }
 @article{gou_yin_he_du_yi_xu_lin_clouse_li_2012, title={Genetic Evidence for an Indispensable Role of Somatic Embryogenesis Receptor Kinases in Brassinosteroid Signaling}, volume={8}, ISSN={["1553-7390"]}, DOI={10.1371/journal.pgen.1002452}, abstractNote={The Arabidopsis thaliana Somatic Embryogenesis Receptor Kinases (SERKs) consist of five members, SERK1 to SERK5, of the leucine-rich repeat receptor-like kinase subfamily II (LRR-RLK II). SERK3 was named BRI1-Associated Receptor Kinase 1 (BAK1) due to its direct interaction with the brassinosteroid (BR) receptor BRI1 in vivo, while SERK4 has also been designated as BAK1-Like 1 (BKK1) for its functionally redundant role with BAK1. Here we provide genetic and biochemical evidence to demonstrate that SERKs are absolutely required for early steps in BR signaling. Overexpression of four of the five SERKs—SERK1, SERK2, SERK3/BAK1, and SERK4/BKK1—suppressed the phenotypes of an intermediate BRI1 mutant, bri1-5. Overexpression of the kinase-dead versions of these four genes in the bri1-5 background, on the other hand, resulted in typical dominant negative phenotypes, resembling those of null BRI1 mutants. We isolated and generated single, double, triple, and quadruple mutants and analyzed their phenotypes in detail. While the quadruple mutant is embryo-lethal, the serk1 bak1 bkk1 triple null mutant exhibits an extreme de-etiolated phenotype similar to a null bri1 mutant. While overexpression of BRI1 can drastically increase hypocotyl growth of wild-type plants, overexpression of BRI1 does not alter hypocotyl growth of the serk1 bak1 bkk1 triple mutant. Biochemical analysis indicated that the phosphorylation level of BRI1 in serk1 bak1 bkk1 is incapable of sensing exogenously applied BR. As a result, the unphosphorylated level of BES1 has lost its sensitivity to the BR treatment in the triple mutant, indicating that the BR signaling pathway has been completely abolished in the triple mutant. These data clearly demonstrate that SERKs are essential to the early events of BR signaling.}, number={1}, journal={PLOS GENETICS}, author={Gou, Xiaoping and Yin, Hongju and He, Kai and Du, Junbo and Yi, Jing and Xu, Shengbao and Lin, Honghui and Clouse, Steven D. and Li, Jia}, year={2012}, month={Jan} }
 @misc{clouse_2011, title={Brassinosteroid signal transduction: from receptor kinase activation to transcriptional networks regulating plant development}, volume={23}, DOI={10.1105/tpc.111.084475}, abstractNote={Brassinosteroid (BR) signal transduction research has progressed rapidly from the initial discovery of the BR receptor to a complete definition of the basic molecular components required to relay the BR signal from perception by receptor kinases at the cell surface to activation of a small family of transcription factors that regulate the expression of more than a thousand genes in a BR-dependent manner. These mechanistic advances have helped answer the intriguing question of how a single molecule, such as a hormone, can have dramatic pleiotropic effects on a broad range of diverse developmental pathways and have shed light on how BRs interact with other plant hormones and environmental cues to shape the growth of the whole plant. This review summarizes the current state of BR signal transduction research and then examines recent articles uncovering gene regulatory networks through which BR influences both vegetative and reproductive development.}, number={4}, journal={Plant Cell}, author={Clouse, S. D.}, year={2011}, pages={1219–1230} }
 @article{oh_sun_oh_zielinski_clouse_huber_2011, title={Enhancing Arabidopsis Leaf Growth by Engineering the BRASSINOSTEROID INSENSITIVE1 Receptor Kinase}, volume={157}, ISSN={["0032-0889"]}, DOI={10.1104/pp.111.182741}, abstractNote={Abstract}, number={1}, journal={PLANT PHYSIOLOGY}, author={Oh, Man-Ho and Sun, Jindong and Oh, Dong Ha and Zielinski, Raymond E. and Clouse, Steven D. and Huber, Steven C.}, year={2011}, month={Sep}, pages={120–131} }
 @article{oh_wang_wu_zhao_clouse_huber_2010, title={Autophosphorylation of Tyr-610 in the receptor kinase BAK1 plays a role in brassinosteroid signaling and basal defense gene expression (Retracted article. See vol. 113, pg. E3987, 2016)}, volume={107}, ISSN={["0027-8424"]}, DOI={10.1073/pnas.0915064107}, abstractNote={
            BAK1 is a leucine-rich repeat receptor-like kinase that functions as a coreceptor with the brassinosteroid (BR) receptor BRI1 and the flagellin receptor FLS2, and as a negative regulator of programmed cell death. BAK1 has been shown to autophosphorylate on numerous serine/threonine sites in vitro as well as to transphosphorylate associated receptor kinases both in vitro and in planta. In the present study we identify Tyr-610 in the carboxyl-terminal domain of BAK1 as a major site of autophosphorylation that is brassinolide-induced in vivo and requires a kinase-active BAK1. Expression of BAK1(Y610F)-Flag in transgenic plants lacking the endogenous
            bak1
            and its functional paralogue,
            bkk1
            , produced plants that were viable but extremely small and generally resembled BR signaling mutants, whereas an acidic substitution for Tyr-610 to mimic phosphorylation restored normal growth. Several lines of evidence support the notion that BR signaling is impaired in the BAK1(Y610F)-Flag plants, and are consistent with the recently proposed sequential transphosphorylation model for BRI1/BAK1 interaction and activation. In contrast, the FLS2-mediated inhibition of seedling growth by the flg22 elicitor occurred normally in the Y610F-directed mutant. However, expression of many defense genes was dramatically reduced in BAK1(Y610F) plants and the nonpathogenic
            hrpA
            mutant of
            Pseudomonas syringae
            was able to grow rapidly in the mutant. These results indicate that phosphorylation of Tyr-610 is required for some but not all functions of BAK1, and adds significantly to the emerging notion that tyrosine phosphorylation could play an important role in plant receptor kinase signaling.
          }, number={41}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Oh, Man-Ho and Wang, Xiaofeng and Wu, Xia and Zhao, Youfu and Clouse, Steven D. and Huber, Steven C.}, year={2010}, month={Oct}, pages={17827–17832} }
 @article{gou_he_yang_yuan_lin_clouse_li_2010, title={Genome-wide cloning and sequence analysis of leucine-rich repeat receptor-like protein kinase genes in Arabidopsis thaliana}, volume={11}, ISSN={["1471-2164"]}, DOI={10.1186/1471-2164-11-19}, abstractNote={Abstract}, journal={BMC GENOMICS}, author={Gou, Xiaoping and He, Kai and Yang, Hui and Yuan, Tong and Lin, Honghui and Clouse, Steven D. and Li, Jia}, year={2010}, month={Jan} }
 @article{mitra_walters_clouse_goshe_2009, title={An Efficient Organic Solvent Based Extraction Method for the Proteomic Analysis of Arabidopsis Plasma Membranes}, volume={8}, ISSN={["1535-3907"]}, DOI={10.1021/pr801044y}, abstractNote={Membrane proteins are involved in diverse cellular processes and are an integral component of many signaling cascades, but due to their highly hydrophobic nature and the complexities associated with studying these proteins in planta, alternative methods are being developed to better characterize these proteins on a proteome-wide scale. In our previous work ( Mitra , S. K. et al. J. Proteome Res. 2007 , 6 , ( 5 ), 1933 - 50 ), methanol-assisted solubilization was determined to facilitate the identification of both hydrophobic and hydrophilic membrane proteins compared to Brij-58 solubilization and was particularly effective for leucine-rich repeat receptor-like kinases (LRR RLKs). To improve peptide identification and to overcome sample losses after tryptic digestion, we have developed an effective chloroform extraction method to promote plasma membrane protein identification. The use of chloroform extraction over traditional solid-phase extraction (SPE) prior to off-line strong cation exchange liquid chromatography (SCXC) and reversed-phase liquid chromatography-tandem mass spectrometry (LC/MS/MS) analysis facilitated the removal of chlorophylls, major contaminants of plant tissue preparations that can affect downstream analysis, in addition to the effective removal of trypsin used in the digestion. On the basis of a statistically derived 5% false discovery rate, the chloroform extraction procedure increased the identification of unique peptides for plasma membrane proteins over SPE by 70% which produced nearly a 2-fold increase in detection of membrane transporters and LRR RLKs without increased identification of contaminating Rubisco and ribosomal peptides. Overall, the combined use of methanol and chloroform provides an effective method to study membrane proteins and can be readily applied to other tissues and cells types for proteomic analysis.}, number={6}, journal={JOURNAL OF PROTEOME RESEARCH}, author={Mitra, Srijeet K. and Walters, Benjamin T. and Clouse, Steven D. and Goshe, Michael B.}, year={2009}, month={Jun}, pages={2752–2767} }
 @article{pereira-netto_roessner_fujioka_bacic_asami_yoshida_clouse_2009, title={Shooting control by brassinosteroids: metabolomic analysis and effect of brassinazole on Malus prunifolia, the Marubakaido apple rootstock}, volume={29}, ISSN={["1758-4469"]}, DOI={10.1093/treephys/tpn052}, abstractNote={To help unravel the role of brassinosteroids (BRs) in the control of shooting, we treated the shoots of Marubakaido apple rootstock (Malus prunifolia (Willd.) Borkh cv. Marubakaido) with brassinolide and Brz 220, an inhibitor of BR biosynthesis. Brassinolide differentially affected elongation and formation of main and primary lateral shoots, which resulted in reduced apical dominance. Treatment of shoots with increasing doses of Brz 220 led to a progressive inhibition of main shoot elongation. Eight different BRs were also identified in the shoots of M. prunifolia. Progressive decline in 6-deoxocathasterone, 6-deoxotyphasterol and castasterone was related to increased doses of Brz 220. Analysis of the metabolic profiles between a fluoro-containing derivative of 28-homocastasterone (5F-HCS) using treated and untreated shoots demonstrated that no 5F-HCS-specific metabolite was identified. However, 4 weeks after the treatment, fructose, glucose and the putatively identified gulonic acid were higher in 5F-HCS-treated shoots, compared to untreated shoots. These results indicate that the previously reported 5F-HCS-induced stimulation of shoot elongation and formation of new shoots in the Marubakaido shoots is under the control of changes in the endogenous BR pool. In addition, the results presented in this report also indicate that the 5F-HCS-induced shooting likely involves a variety of different mechanisms and consequently does not result from changes in the endogenous levels of any single metabolite.}, number={4}, journal={TREE PHYSIOLOGY}, author={Pereira-Netto, Adaucto B. and Roessner, Ute and Fujioka, Shozo and Bacic, Antony and Asami, Tadao and Yoshida, Shigeo and Clouse, Steven D.}, year={2009}, month={Apr}, pages={607–620} }
 @article{malinowski_higgins_luo_piper_nazir_bajwa_clouse_thompson_stratmann_2009, title={The tomato brassinosteroid receptor BRI1 increases binding of systemin to tobacco plasma membranes, but is not involved in systemin signaling}, volume={70}, ISSN={["1573-5028"]}, DOI={10.1007/s11103-009-9494-x}, abstractNote={The tomato wound signal systemin is perceived by a specific high-affinity, saturable, and reversible cell surface receptor. This receptor was identified as the receptor-like kinase SR160, which turned out to be identical to the brassinosteroid receptor BRI1. Recently, it has been shown that the tomato bri1 null mutant cu3 is as sensitive to systemin as wild type plants. Here we explored these contradictory findings by studying the responses of tobacco plants (Nicotiana tabacum) to systemin. A fluorescently-labeled systemin analog bound specifically to plasma membranes of tobacco suspension-cultured cells that expressed the tomato BRI1-FLAG transgene, but not to wild type tobacco cells. On the other hand, signaling responses to systemin, such as activation of mitogen-activated protein kinases and medium alkalinization, were neither increased in BRI1-FLAG-overexpressing tobacco cells nor decreased in BRI1-silenced cells as compared to levels in untransformed control cells. Furthermore, in transgenic tobacco plants BRI1-FLAG became phosphorylated on threonine residues in response to brassinolide application, but not in response to systemin. When BRI1 transcript levels were reduced by virus-induced gene silencing in tomato plants, the silenced plants displayed a phenotype characteristic of bri1 mutants. However, their response to overexpression of the Prosystemin transgene was the same as in control plants. Taken together, our data suggest that BRI1 can function as a systemin binding protein, but that binding of the ligand does not transduce the signal into the cell. This unusual behavior and the nature of the elusive systemin receptor will be discussed.}, number={5}, journal={PLANT MOLECULAR BIOLOGY}, author={Malinowski, Robert and Higgins, Rebecca and Luo, Yuan and Piper, Laverne and Nazir, Azka and Bajwa, Vikramjit S. and Clouse, Steven D. and Thompson, Paul R. and Stratmann, Johannes W.}, year={2009}, month={Jul}, pages={603–616} }
 @article{oh_wang_kota_goshe_clouse_huber_2009, title={Tyrosine phosphorylation of the BRI1 receptor kinase emerges as a component of brassinosteroid signaling in Arabidopsis}, volume={106}, ISSN={["0027-8424"]}, DOI={10.1073/pnas.0810249106}, abstractNote={
            Brassinosteroids (BRs) are essential growth-promoting hormones that regulate many aspects of plant growth and development. Two leucine-rich repeat receptor-like kinases (LRR-RLKs) are involved in BR perception and signal transduction: brassinosteroid insensitive 1 (BRI1), which is the BR receptor, and its coreceptor BRI1-associated kinase 1 (BAK1). Both proteins are classified as serine/threonine protein kinases, but here we report that recombinant cytoplasmic domains of BRI1 and BAK1 also autophosphorylate on tyrosine residues and thus are dual-specificity kinases. With BRI1, Tyr-831 and Tyr-956 are identified as autophosphorylation sites in vitro and in vivo. Interestingly, Tyr-956 in kinase subdomain V is essential for activity, because the Y956F mutant is catalytically inactive and thus this site cannot be simply manipulated by mutagenesis. In contrast, Tyr-831 in the juxtamembrane domain is not essential for kinase activity but plays an important role in BR signaling in vivo, because expression of BRI1(Y831F)-Flag in transgenic
            bri1–5
            plants results in plants with larger leaves (but altered leaf shape) and early flowering relative to plants expressing wild-type BRI1-Flag. Acidic substitutions of Tyr-831 restored normal leaf size (but not shape) and normal flowering time. This is an example where a specific tyrosine residue has been shown to play an important role in vivo in plant receptor kinase function. Interestingly, 6 additional LRR-RLKs (of the 23 tested) were also found to autophosphorylate on tyrosine in addition to serine and threonine, suggesting that tyrosine signaling should be considered with other plant receptor kinases as well.
          }, number={2}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Oh, Man-Ho and Wang, Xiaofeng and Kota, Uma and Goshe, Michael B. and Clouse, Steven D. and Huber, Steven C.}, year={2009}, month={Jan}, pages={658–663} }
 @article{wang_kota_he_blackburn_li_goshe_huber_clouse_2008, title={Sequential transphosphorylation of the BRI1/BAK1 receptor kinase complex impacts early events in brassinosteroid signaling}, volume={15}, ISSN={["1534-5807"]}, DOI={10.1016/j.devcel.2008.06.011}, abstractNote={Brassinosteroids (BRs) regulate plant development through a signal transduction pathway involving the BRI1 and BAK1 transmembrane receptor kinases. The detailed molecular mechanisms of phosphorylation, kinase activation, and oligomerization of the BRI1/BAK1 complex in response to BRs are uncertain. We demonstrate that BR-dependent activation of BRI1 precedes association with BAK1 in planta, and that BRI1 positively regulates BAK1 phosphorylation levels in vivo. BRI1 transphosphorylates BAK1 in vitro on specific kinase-domain residues critical for BAK1 function. BAK1 also transphosphorylates BRI1, thereby quantitatively increasing BRI1 kinase activity toward a specific substrate. We propose a sequential transphosphorylation model in which BRI1 controls signaling specificity by direct BR binding followed by substrate phosphorylation. The coreceptor BAK1 is then activated by BRI1-dependent transphosphorylation and subsequently enhances signaling output through reciprocal BRI1 transphosphorylation. This model suggests both conservation and distinct differences between the molecular mechanisms regulating phosphorylation-dependent kinase activation in plant and animal receptor kinases.}, number={2}, journal={DEVELOPMENTAL CELL}, author={Wang, Xiaofeng and Kota, Uma and He, Kai and Blackburn, Kevin and Li, Jia and Goshe, Michael B. and Huber, Steven C. and Clouse, Steven D.}, year={2008}, month={Aug}, pages={220–235} }
 @article{clouse_2008, title={The molecular intersection of brassinosteroid-regulated growth and flowering in Arabidopsis}, volume={105}, ISSN={["0027-8424"]}, DOI={10.1073/pnas.0803552105}, abstractNote={The transition from vegetative to reproductive growth in plants is a major developmental switch regulated by a set of complex, integrated signal transduction pathways that respond to both environmental cues and endogenous signals to alter the expression of genes associated with the initiation and development of floral organs (1). Understanding the molecular mechanisms of flowering has both intrinsic scientific interest and immense practical agricultural applications. In many plants, the timing of flowering is regulated by light quality and quantity, temperature, and the action of gibberellins (GAs), a class of plant hormones with pleiotropic effects on both vegetative and reproductive development (2). Another class of plant hormones, the brassinosteroids (BRs), also regulates multiple aspects of plant development (3), and recent evidence suggests that BRs stimulate flowering by reducing transcript levels of a potent floral repressor (4). As with many other developmental processes in plants, our understanding of molecular events underlying floral initiation has been greatly advanced by studying mutants in the model plant Arabidopsis thaliana. The molecular genetic analysis of Arabidopsis mutants exhibiting early or delayed flowering has uncovered numerous critical components of signal transduction pathways regulating response to photoperiod, hormones, and cold treatment. Similarly, analysis of mutants with defective BR perception or response has provided extensive details on the molecular components required for BR signaling (5, 6). In this issue of PNAS, Yu et al. (7) provide a connection between BR signal transduction and pathways controlling floral initiation by demonstrating that a critical …}, number={21}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Clouse, Steven D.}, year={2008}, month={May}, pages={7345–7346} }
 @article{mitra_gantt_ruby_clouse_goshe_2007, title={Membrane proteomic analysis of Arabidopsis thaliana using alternative solubilization techniques}, volume={6}, ISSN={["1535-3907"]}, DOI={10.1021/pr060525b}, abstractNote={This study presents a comparative proteomic analysis of the membrane subproteome of whole Arabidopsis seedlings using 2% Brij-58 or 60% methanol to enrich and solubilize membrane proteins for strong cation exchange fractionation and reversed-phase liquid chromatography-tandem mass spectrometry (LC-MS/MS). A total of 441 proteins were identified by our Brij-58 method, and 300 proteins were detected by our methanol-based solubilization approach. Although the total number of proteins obtained using the nonionic detergent was higher than the total obtained by organic solvent, the ratio of predicted membrane proteins to total proteins identified indicates up to an 18.6% greater enrichment efficiency using methanol. Using two different bioinformatics approaches, between 31.0 and 40.0% of the total proteins identified by the methanol-based method were classified as containing at least one putative transmembrane domain as compared to 22.0-23.4% for Brij-58. In terms of protein hydrophobicity as determined by the GRAVY index, it was revealed that methanol was more effective than Brij-58 for solubilizing membrane proteins ranging from -0.4 (hydrophilic) to +0.4 (hydrophobic). Methanol was also approximately 3-fold more effective than Brij-58 in identifying leucine-rich repeat receptor-like kinases. The ability of methanol to effectively solubilize and denature both hydrophobic and hydrophilic proteins was demonstrated using bacteriorhodopsin and cytochrome c, respectively, where both proteins were identified with at least 82% sequence coverage from a single reversed-phase LC-MS/MS analysis. Overall, our data show that methanol is a better alternative for identifying a wider range of membrane proteins than the nonionic detergent Brij-58.}, number={5}, journal={JOURNAL OF PROTEOME RESEARCH}, author={Mitra, Srijeet K. and Gantt, John A. and Ruby, James F. and Clouse, Steven D. and Goshe, Michael B.}, year={2007}, pages={1933–1950} }
 @article{wang_goshe_soderblom_phinney_kuchar_li_asami_yoshida_huber_clouse_2005, title={Identification and functional analysis of in vivo phosphorylation sites of the Arabidopsis BRASSINOSTEROID-INSENSITIVE1 receptor kinase}, volume={17}, ISSN={["1532-298X"]}, DOI={10.1105/tpc.105.031393}, abstractNote={Brassinosteroids (BRs) regulate multiple aspects of plant growth and development and require an active BRASSINOSTEROID-INSENSITIVE1 (BRI1) and BRI1-ASSOCIATED RECEPTOR KINASE1 (BAK1) for hormone perception and signal transduction. Many animal receptor kinases exhibit ligand-dependent oligomerization followed by autophosphorylation and activation of the intracellular kinase domain. To determine if early events in BR signaling share this mechanism, we used coimmunoprecipitation of epitope-tagged proteins to show that in vivo association of BRI1 and BAK1 was affected by endogenous and exogenous BR levels and that phosphorylation of both BRI1 and BAK1 on Thr residues was BR dependent. Immunoprecipitation of epitope-tagged BRI1 from Arabidopsis thaliana followed by liquid chromatography-tandem mass spectrometry (LC/MS/MS) identified S-838, S-858, T-872, and T-880 in the juxtamembrane region, T-982 in the kinase domain, and S-1168 in C-terminal region as in vivo phosphorylation sites of BRI1. MS analysis also strongly suggested that an additional two residues in the juxtamembrane region and three sites in the activation loop of kinase subdomain VII/VIII were phosphorylated in vivo. We also identified four specific BAK1 autophosphorylation sites in vitro using LC/MS/MS. Site-directed mutagenesis of identified and predicted BRI1 phosphorylation sites revealed that the highly conserved activation loop residue T-1049 and either S-1044 or T-1045 were essential for kinase function in vitro and normal BRI1 signaling in planta. Mutations in the juxtamembrane or C-terminal regions had only small observable effects on autophosphorylation and in planta signaling but dramatically affected phosphorylation of a peptide substrate in vitro. These findings are consistent with many aspects of the animal receptor kinase model in which ligand-dependent autophosphorylation of the activation loop generates a functional kinase, whereas phosphorylation of noncatalytic intracellular domains is required for recognition and/or phosphorylation of downstream substrates.}, number={6}, journal={PLANT CELL}, author={Wang, XF and Goshe, MB and Soderblom, EJ and Phinney, BS and Kuchar, JA and Li, J and Asami, T and Yoshida, S and Huber, SC and Clouse, SD}, year={2005}, month={Jun}, pages={1685–1703} }
 @article{ehsan_ray_phinney_wang_huber_clouse_2005, title={Interaction of Arabidopsis BRASSINOSTEROID-INSENSITIVE 1 receptor kinase with a homolog of mammalian TGF-beta receptor interacting protein}, volume={43}, ISSN={["1365-313X"]}, DOI={10.1111/j.1365-313X.2005.02448.x}, abstractNote={Summary}, number={2}, journal={PLANT JOURNAL}, author={Ehsan, H and Ray, WK and Phinney, B and Wang, XF and Huber, SC and Clouse, SD}, year={2005}, month={Jul}, pages={251–261} }
 @article{sebastia_hardin_clouse_kieber_huber_2004, title={Identification of a new motif for CDPK phosphorylation in vitro that suggests ACC synthase may be a CDPK substrate}, volume={428}, ISSN={["1096-0384"]}, DOI={10.1016/j.abb.2004.04.025}, abstractNote={1-Amino-cyclopropane-1-carboxylate synthase (ACS) catalyzes the rate-determining step in the biosynthesis of the plant hormone ethylene, and there is evidence for regulation of stability of the protein by reversible protein phosphorylation. The site of phosphorylation of the tomato enzyme, LeACS2, was recently reported to be Ser460, but the requisite protein kinase has not been identified. In the present study, a synthetic peptide based on the known regulatory phosphorylation site (KKNNLRLS460FSKRMY) in LeACS2 was found to be readily phosphorylated in vitro by several calcium-dependent protein kinases (CDPKs), but not a plant SNF1-related protein kinase or the kinase domain of the receptor-like kinase, BRI1, involved in brassinosteroid signaling. Studies with variants of the LeACS2-Ser460 peptide establish a fundamentally new phosphorylation motif that is broadly targeted by CDPKs: φ−1-[ST]0-φ+1-X-Basic+3-Basic+4, where φ is a hydrophobic residue. Database analysis using the new motif predicts a number of novel phosphorylation sites in plant proteins. Finally, we also demonstrate that CDPKs and SnRK1s do not recognize motifs presented in the reverse order, indicating that side chain interactions alone are not sufficient for substrate recognition.}, number={1}, journal={ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS}, author={Sebastia, CH and Hardin, SC and Clouse, SD and Kieber, JJ and Huber, SC}, year={2004}, month={Aug}, pages={81–91} }
 @misc{oh_clouse_2003, title={Brassinosteroids: Modes of BR action and signal transduction}, volume={46}, ISSN={["1867-0725"]}, DOI={10.1007/bf03030294}, number={1}, journal={JOURNAL OF PLANT BIOLOGY}, author={Oh, MH and Clouse, SD}, year={2003}, month={Mar}, pages={1–9} }
 @article{clouse_2003, title={Recent advances in brassinosteroid research: From molecular mechanisms to practical applications}, volume={22}, ISSN={["0721-7595"]}, DOI={10.1007/s00344-003-0067-y}, number={4}, journal={JOURNAL OF PLANT GROWTH REGULATION}, author={Clouse, SD}, year={2003}, month={Dec}, pages={273–275} }
 @article{clouse_2002, title={Arabidopsis mutants reveal multiple roles for sterols in plant development}, volume={14}, ISSN={["1040-4651"]}, DOI={10.1105/tpc.140930}, abstractNote={The molecular genetic, and biochemical analysis of sterol-deficient mutants in Arabidopsis strongly suggests an essential role for sterols in regulating multiple events in plant development, independent of their conversion to brassinosteroids (BRs). Embryogenesis, cell elongation, vascular}, number={9}, journal={PLANT CELL}, author={Clouse, SD}, year={2002}, month={Sep}, pages={1995–2000} }
 @misc{clouse_2002, title={Brassinosteroid signal transduction: Clarifying the pathway from ligand perception to gene expression}, volume={10}, ISSN={["1097-2765"]}, DOI={10.1016/S1097-2765(02)00744-X}, abstractNote={Recent genetic screens for novel components of brassinosteroid signaling have revealed proteins with cell surface, cytoplasmic, and nuclear localization that function as either positive activators or negative regulators of the brassinosteroid response. Initial microarray experiments have expanded the number of known brassinosteroid-regulated genes, providing a useful resource for better understanding terminal events in signal transduction.}, number={5}, journal={MOLECULAR CELL}, author={Clouse, SD}, year={2002}, month={Nov}, pages={973–982} }
 @article{clouse_2002, title={Brassinosteroid signaling: Novel downstream components emerge}, volume={12}, ISSN={["0960-9822"]}, DOI={10.1016/S0960-9822(02)00964-8}, abstractNote={Continued genetic screening and analysis of Arabidopsis mutants has extended our view of brassinosteroid signaling beyond hormone perception to downstream events involving a negative cytoplasmic regulator and nuclear localized positive activators of the brassinosteroid response.}, number={14}, journal={CURRENT BIOLOGY}, author={Clouse, SD}, year={2002}, month={Jul}, pages={R485–R487} }
 @misc{clouse_2002, title={Brassinosteroids - Plant counterparts to animal steroid hormones?}, volume={65}, ISBN={["0-12-709865-8"]}, ISSN={["0083-6729"]}, DOI={10.1016/S0083-6729(02)65065-4}, abstractNote={Brassinosteroids are polyhydroxylated derivatives of common plant membrane sterols such as campesterol. They occur throughout the plant kingdom and have been shown by genetic and biochemical analyses to be essential for normal plant growth and development. Numerous reviews have detailed the recent progress in our understanding of the biosynthesis, physiological responses, and molecular modes of action of brassinosteroids. It is clear that like their animal steroid counterparts, brassinosteroids have a defined receptor, can regulate the expression of specific genes, and can orchestrate complex physiological responses involved in growth. This review summarizes the current status of BR research, pointing out where appropriate the similarities and differences between the mechanism of action of brassinosteroids and the more thoroughly studied animal steroid hormones.}, journal={VITAMINS AND HORMONES - ADVANCES IN RESEARCH AND APPLICATIONS, VOL 65}, author={Clouse, SD}, year={2002}, pages={195–223} }
 @article{iliev_xu_polisensky_oh_torisky_clouse_braam_2002, title={Transcriptional and posttranscriptional regulation of Arabidopsis TCH4 expression by diverse stimuli. Roles of cis regions and brassinosteroids}, volume={130}, ISSN={["0032-0889"]}, DOI={10.1104/pp.008680}, abstractNote={Abstract}, number={2}, journal={PLANT PHYSIOLOGY}, author={Iliev, EA and Xu, W and Polisensky, DH and Oh, MH and Torisky, RS and Clouse, SD and Braam, J}, year={2002}, month={Oct}, pages={770–783} }
 @article{clouse_2001, title={Brassinosteroids}, volume={11}, ISSN={["0960-9822"]}, DOI={10.1016/s0960-9822(01)00549-8}, abstractNote={What are they? Brassinosteroids are polyhydroxlyated sterol derivatives with close structural similarity to animal and insect steroid hormones. They occur at low levels throughout the plant kingdom and regulate the expansion, division and differentiation of cells in young growing tissues. More than 40 brassinosteroids have been identified and characterized from various plant organs, including pollen, seeds, and vegetative shoots. How were they discovered? Researchers at the US Department of Agriculture showed that organic extracts of Brassica napus pollen strongly stimulated cell elongation and division in a bean second-internode assay. The structure of the active component of the B. napus extract was characterized in 1979 and found to be a 28 carbon steroid, given the name brassinolide. Many chemically related compounds have been identified in a range of plant species, and are named brassinosteroids. Brassinolide is the most active and many brassinosteroids are precursors or metabolic products of brassinolide. How are they made? Brassinolide is derived from the membrane sterol campesterol through a series of reductions, hydroxylations, epimerizations and oxidations. There are two major branches of the pathway, termed early and late C-6 oxidation, depending on whether a ketone at carbon 6 is added before or after side chain hydroxylation. Recent evidence suggests that the pathway is more of a metabolic grid than two distinct branches. Many of the genes encoding brassinosteroid biosynthetic enzymes have been cloned in Arabidopsis thaliana and mutants blocking several biosynthetic steps have been identified in Arabidopsis, pea and tomato. How do they work? A complete understanding of the molecular mechanism of brassinosteroid action is still several years away and is a pressing research priority in many laboratories. During cell elongation, a good deal of evidence suggests that brassinosteroids affect the mechanical properties of cell walls, via genomic and non-genomic pathways, to allow turgor-driven cell expansion to proceed. The phenotypes of brassinosteroid-deficient and insensitive mutants confirm that brassinosteroids are essential for cell elongation and also suggest a role in vascular differentiation, senescence, fertility, leaf morphology and light–dark regulation of development. Is there a receptor? The BRI1 gene of Arabidopsis encodes a leucine-rich repeat receptor kinase that has many of the properties expected of a brassinosteroid receptor, or at least a critical component of a receptor complex. Mutations in this gene result in severe developmental phenotypes and biochemical studies have shown that overexpression results in increased binding of labeled brassinosteroid at the cell surface. Whether BRI1 binds brassinosteroid directly or in the presence of another sterol binding protein is unknown. Ligand binding by the extracellular domain of receptor kinases results in autophosphorylation and activation of the intracellular kinase domain. This is followed by phosphorylation of downstream components of the signal transduction pathways. Several substrates of the BRI1 kinase domain have been identified in vitro and experiments are underway to verify if these are indeed in vivo interacting partners of BRI1. Interestingly, plants have conserved the steroid signal but not the classical animal-type intracellular steroid receptor signaling pathway. Do they have commercial potential? Spraying brassinosteroid on a variety of crops including wheat, rice, corn, melons, potatoes, oranges, grapes and pears has in some cases dramaticaly increased yields. Brassinosteroids apparently have more effect when plants are under stress than when grown under optimal conditions. Structurally modified brassinosteroids with greater stability under field conditions have been synthesized and tested in Japan. An inhibitor of brassinosteroid biosynthesis, brassinazole, has also been discovered in Japan and may have some practical utility in slowing plant growth. Where can I find out more?}, number={22}, journal={CURRENT BIOLOGY}, author={Clouse, S}, year={2001}, month={Nov}, pages={R904–R904} }
 @article{jiang_clouse_2001, title={Expression of a plant gene with sequence similarity to animal TGF-beta receptor interacting protein is regulated by brassinosteroids and required for normal plant development}, volume={26}, ISSN={["0960-7412"]}, DOI={10.1046/j.1365-313x.2001.01007.x}, abstractNote={Summary}, number={1}, journal={PLANT JOURNAL}, author={Jiang, JR and Clouse, SD}, year={2001}, month={Apr}, pages={35–45} }
 @misc{clouse_2001, title={Integration of light and brassinosteroid signals in etiolated seedling growth}, volume={6}, ISSN={["1360-1385"]}, DOI={10.1016/S1360-1385(01)02102-1}, abstractNote={<h2>Abstract</h2> Light and brassinosteroids are involved in the regulation of stem elongation in etiolated seedlings, but the molecular mechanism of their integration is not clear. Recent work in pea has shown that the dark-inducible, light-repressible small G protein, Pra2, interacts with and activates a cytochrome P450 C-2 hydroxylase involved in brassinolide biosynthesis. Thus, a novel link between light signal transduction and the endogenous levels of an important growth-promoting plant hormone has been established.}, number={10}, journal={TRENDS IN PLANT SCIENCE}, author={Clouse, SD}, year={2001}, month={Oct}, pages={443–445} }
 @article{koka_cerny_gardner_noguchi_fujioka_takatsuto_yoshida_clouse_2000, title={A putative role for the tomato genes DUMPY and CURL-3 in brassinosteroid biosynthesis and response}, volume={122}, ISSN={["0032-0889"]}, DOI={10.1104/pp.122.1.85}, abstractNote={Abstract}, number={1}, journal={PLANT PHYSIOLOGY}, author={Koka, CV and Cerny, RE and Gardner, RG and Noguchi, T and Fujioka, S and Takatsuto, S and Yoshida, S and Clouse, SD}, year={2000}, month={Jan}, pages={85–98} }
 @article{clouse_2000, title={Plant development: A role for sterols in embryogenesis}, volume={10}, DOI={10.1016/S0960-9822(00)00639-4}, abstractNote={The Arabidopsis mutants fackel and sterol methyltransferase 1 have defects associated with body organization of the seedling. Molecular analysis of these mutants has revealed that plant sterols may be key signaling molecules influencing position-dependent cell fate during embryonic development.}, number={16}, journal={Current Biology}, author={Clouse, S. D.}, year={2000}, pages={R601–604} }
 @article{oh_ray_huber_asara_gage_clouse_2000, title={Recombinant brassinosteroid insensitive 1 receptor-like kinase autophosphorylates on serine and threonine residues and phosphorylates a conserved peptide motif in vitro}, volume={124}, ISSN={["1532-2548"]}, DOI={10.1104/pp.124.2.751}, abstractNote={Abstract}, number={2}, journal={PLANT PHYSIOLOGY}, author={Oh, MH and Ray, WK and Huber, SC and Asara, JM and Gage, DA and Clouse, SD}, year={2000}, month={Oct}, pages={751–765} }
 @article{mussig_kauschmann_clouse_altmann_2000, title={The Arabidopsis PHD-finger protein SHL is required for proper development and fertility}, volume={264}, ISSN={["0026-8925"]}, DOI={10.1007/s004380000313}, abstractNote={The SHL gene from Arabidopsis thaliana encodes a small nuclear protein that contains a BAH domain and a PHD finger. Both domains are found in numerous (putative) transcriptional regulators and chromatin-remodeling factors. Different sets of transgenic lines were established to analyze the physiological relevance of SHL. SHL expression driven by the CaMV 35S promoter results in reduced growth, early flowering, early senescence, and impaired flower and seed formation. Antisense inhibition of SHL expression gives rise to dwarfism and delayed development. In-frame N-terminal fusion of the SHL protein to beta-glucuronidase (GUS) directs GUS to the nucleus of stably transformed Arabidopsis plants. Thus, SHL encodes a novel putative regulator of gene expression, which directly or indirectly influences a broad range of developmental processes.}, number={4}, journal={MOLECULAR AND GENERAL GENETICS}, author={Mussig, C and Kauschmann, A and Clouse, SD and Altmann, T}, year={2000}, month={Nov}, pages={363–370} }
 @article{oh_clouse_1998, title={Brassinolide affects the rate of cell division in isolated leaf protoplasts of Petunia hybrida}, volume={17}, ISSN={["1432-203X"]}, DOI={10.1007/s002990050510}, abstractNote={Brassinosteroids are known to promote cell elongation in a wide range of plant species but their effect on cell division has not been as extensively studied. We examined the effect of brassinolide on the kinetics and final division frequencies of regenerating leaf mesophyll protoplasts of Petunia hybrida Vilm v. Comanche. Under optimal auxin and cytokinin conditions, 10-100 nM brassinolide accelerated the time of first cell division by 12 h but had little effect on the final division frequencies after 72-120 h of culture. One micromolar brassinolide showed the same acceleration of first cell division but inhibited the final division frequency by approximately 20%. Under sub-optimal auxin conditions, 10-100 nM brassinolide both accelerated the time of first cell division and dramatically increased the 72- to 120-h final division frequencies. Isolated protoplasts may provide a useful model system to investigate the molecular mechanisms of brassinosteroid action on cell proliferation.}, number={12}, journal={PLANT CELL REPORTS}, author={Oh, MH and Clouse, SD}, year={1998}, month={Sep}, pages={921–924} }
 @misc{clouse_sasse_1998, title={Brassinosteroids: Essential regulators of plant growth and development}, volume={49}, ISSN={["1040-2519"]}, DOI={10.1146/annurev.arplant.49.1.427}, abstractNote={▪ Abstract  Brassinosteroids (BRs) are growth-promoting natural products found at low levels in pollen, seeds, and young vegetative tissues throughout the plant kingdom. Detailed studies of BR biosynthesis and metabolism, coupled with the recent identification of BR-insensitive and BR-deficient mutants, has greatly expanded our view of steroids as signals controlling plant growth and development. This review examines the microchemical and molecular genetic analyses that have provided convincing evidence for an essential role of BRs in diverse developmental programs, including cell expansion, vascular differentiation, etiolation, and reproductive development. Recent advances relevant to the molecular mechanisms of BR-regulated gene expression and BR signal transduction are also discussed.}, journal={ANNUAL REVIEW OF PLANT PHYSIOLOGY AND PLANT MOLECULAR BIOLOGY}, author={Clouse, SD and Sasse, JM}, year={1998}, pages={427–451} }
 @book{sakurai_yokota_clouse_1998, title={Brassinosteroids: Steroidal plant hormones}, ISBN={4431702148}, publisher={Tokyo & New York: Springer-Verlag}, author={Sakurai, A. and Yokota, T. and Clouse, S. D.}, year={1998} }
 @article{oh_romanow_smith_zamski_sasse_clouse_1998, title={Soybean BRU1 encodes a functional xyloglucan endotransglycosylase that is highly expressed in inner epicotyl tissues during brassinosteroid-promoted elongation}, volume={39}, ISSN={["1471-9053"]}, DOI={10.1093/oxfordjournals.pcp.a029283}, abstractNote={Brassinosteroids promote soybean epicotyl elongation and regulate expression of BRU1, a gene with homology to xyloglucan endotransglycosylases (XETs). Recombinant BRU1 protein possesses XET activity and in situ hybridization reveals highest BRUl transcript accumulation in inner epicotyl tissue, particularly the phloem and paratracheary parenchyma cells. These results suggest a role for BRUl in vascular development in addition to cell elongation.}, number={1}, journal={PLANT AND CELL PHYSIOLOGY}, author={Oh, MH and Romanow, WG and Smith, RC and Zamski, E and Sasse, J and Clouse, SD}, year={1998}, month={Jan}, pages={124–130} }
 @article{clouse_1997, title={Molecular genetic analysis of brassinosteroid action}, volume={100}, ISSN={["1399-3054"]}, DOI={10.1111/j.1399-3054.1997.tb03077.x}, abstractNote={Recent applications of molecular techniques to the study of brassinosteroid action have enhanced our understanding of these unique plant growth regulators. The cloning of genes regulated by brassinosteroids has revealed novel information on the control of gene expression by plant steroids and has extended our knowledge of brassinosteroid‐promoted cell expansion. The analysis of brassinosteroid‐deficient and brassinosteroid‐insensitive mutants has implicated these growth regulators in a number of essential developmental programs including organ elongation, leaf development, photomorphogenesis, fertility, apical dominance and vascular differentiation.}, number={3}, journal={PHYSIOLOGIA PLANTARUM}, author={Clouse, SD}, year={1997}, month={Jul}, pages={702–709} }
 @article{clouse_langford_mcmorris_1996, title={A brassinosteroid-insensitive mutant in Arabidopsis thaliana exhibits multiple defects in growth and development}, volume={111}, DOI={10.1104/pp.111.3.671}, abstractNote={Abstract}, number={3}, journal={Plant Physiology}, author={Clouse, S. D. and Langford, M. and McMorris, T. C.}, year={1996}, pages={671–678} }
 @article{clouse_1996, title={Plant hormones: Brassinosteroids in the spotlight}, volume={6}, ISSN={["1879-0445"]}, DOI={10.1016/S0960-9822(09)00442-4}, abstractNote={Recent studies on dwarf mutants of the model plant Arabidopsis thallana have provided convincing evidence that brassinosteroids-natural plant products similar to animal steroid hormones-are essential for normal plant growth and development.}, number={6}, journal={CURRENT BIOLOGY}, author={Clouse, SD}, year={1996}, month={Jun}, pages={658–661} }