Recombinant brassinosteroid insensitive 1 receptor-like kinase autophosphorylates on serine and threonine residues and phosphorylates a conserved peptide motif in vitro

CKL2 mediates the crosstalk between abscisic acid and brassinosteroid signaling to promote swift growth recovery after stress in Arabidopsis

Plants must adapt to the constantly changing environment. Adverse environmental conditions trigger various defensive responses, including growth inhibition mediated by phytohormone abscisic acid (ABA). When the stress recedes, plants must transit rapidly from stress defense to growth recovery, but the underlying mechanisms by which plants switch promptly and accurately between stress resistance and growth are poorly understood. Here, using quantitative phosphoproteomics strategy, we discovered that early ABA signaling activates upstream components of brassinosteroid (BR) signaling through CASEIN KINASE 1-LIKE PROTEIN 2 (CKL2). Further investigations showed that CKL2 interacts with and phosphorylates BRASSINOSTEROID INSENSITIVE1 (BRI1), the main BR receptor, to maintain the basal activity of the upstream of BR pathway in plants exposed to continuous stress conditions. When stress recedes, the elevated phosphorylation of BRI1 by CKL2 contributes to the swift reactivation of BR signaling, which results in quick growth recovery. These results suggest that CKL2 plays a critical regulatory role in the rapid switch between growth and stress resistance. Our evidence expands the understanding of how plants modulate stress defense and growth by integrating ABA and BR signaling cascades.

Identification of Feronia-interacting proteins in Arabidopsis thaliana

BACKGROUND

Plant growth and development are complex processes modulated by numerous genes, transcription factors, hormones, and peptides. Several reports implicate the membrane-localized Catharanthus roseus receptor-like kinase1 (CrRLK1L) protein, FERONIA (FER), involved in plant development. However, protein targets of FER remain poorly characterized.

OBJECTIVE

FER recombinant proteins were analyzed, and FER-interacting proteins were identified, to better understand the function of the Arabidopsis thaliana FER (AtFER) gene in plant development.

METHODS

AtFER-interacting proteins were identified through Yeast-Two Hybrid (Y2H) and validated by bimolecular fluorescence complementation (BiFC). Autophosphorylation activity was evaluated in AtFER site-directed and deletion mutants.

RESULTS

AtFER cytoplasmic kinase domain (Flag-FER-CD) is autophosphorylated at the Thr residue (s), with T559 and T664 as important sites for AtFER kinase activity. In addition, the carboxy terminal region is essential for AtFER kinase activity. Y2H identified an Armadillo (ARM)-repeat protein (At4g16490) with tandem copies of a degenerate protein sequence motif, a U-BOX 9 (PUB9, At3g07360), IQ-DOMAIN 7 (IQD7, At1g17480), and heteroglycan glucosidase 1 (HGL1, At3g23640) as AtFER-interacting proteins. BiFC confirmed the in vivo interactions between these four proteins and AtFER in tobacco (Nicotiana benthamiana) leaf transient expression assays. The RAPID ALKALINIZATION FACTOR1 (RALF1) peptide, which is a FER ligand, induced the expression of genes encoding the four AtFER-interacting proteins.

CONCLUSION

The AtFER-interacting proteins identified in this study are likely involved in FER-mediated intracellular signaling pathways that are essential in plant growth and development, and possibly plant immunity.

Crystal structure of the phosphorylated Arabidopsis MKK5 reveals activation mechanism of MAPK kinases

The mitogen-activated protein kinase (MAPK) signaling pathways are highly conserved in eukaryotes, regulating various cellular processes. The MAPK kinases (MKKs) are dual specificity kinases, serving as convergence and divergence points of the tripartite MAPK cascades. Here, we investigate the biochemical characteristics and three-dimensional structure of MKK5 in Arabidopsis (AtMKK5). The recombinant full-length AtMKK5 is phosphorylated and can activate its physiological substrate AtMPK6. There is a conserved kinase interacting motif (KIM) at the N-terminus of AtMKK5, indispensable for specific recognition of AtMPK6. The kinase domain of AtMKK5 adopts active conformation, of which the extended activation segment is stabilized by the phosphorylated Ser221 and Thr215 residues. In line with sequence divergence from other MKKs, the αD and αK helices are missing in AtMKK5, suggesting that the AtMKK5 may adopt distinct modes of upstream kinase/substrate binding. Our data shed lights on the molecular mechanisms of MKK activation and substrate recognition, which may help design specific inhibitors targeting human and plant MKKs.

Role of tyrosine autophosphorylation and methionine residues in BRI1 function in Arabidopsis thaliana

BACKGROUND

Brassinosteroids (BRs), a group of plant growth hormones, control biomass accumulation and biotic and abiotic stress tolerance, and therefore are highly relevant to agriculture. BRs bind to the BR receptor protein, brassinosteroid insensitive 1 (BRI1), which is classified as a serine/threonine (Ser/Thr) protein kinase. Recently, we reported that BRI1 acts as a dual-specificity kinase both in vitro and in vivo by undergoing autophosphorylation at tyrosine (Tyr) residues.

OBJECTIVE

In this study, we characterized the increased leaf growth and early flowering phenotypes of transgenic lines expressing the mutated recombinant protein, BRI1(Y831F)-Flag, compared with those expressing BRI1-Flag. BRI1(Y831F)-Flag transgenic plants showed a reduction in hypocotyl and petiole length compared with BRI1-Flag seedlings. Transcriptome analysis revealed differential expression of flowering time-associated genes (AP1, AP2, AG, FLC, and SMZ) between BRI1(Y831F)-Flag and BRI1-Flag transgenic seedlings. We also performed site-directed mutagenesis of the BRI1 gene, and investigated the effect of methionine (Met) substitution in the extracellular domain (ECD) of BRI1 on plant growth and BR sensitivity by evaluating hypocotyl elongation and root growth inhibition.

METHODS

The pBIB-Hyg⁺-pBR-BRI1-Flag construct(Li et al. 2002) was used as the template for SDM with QuickChange XL Site Directed Mutagenesis Kit (Stratagene, La Jolla, CA, USA) to make the SDM mutants. After PCR with SDM kit, add 1 μl of Dpn1 to PCR reaction. Incubate at 37 °C for 2 h to digest parental DNA and then transformed into XL10-gold competent cells. Transcriptome analysis was carried out at the University of Illinois (Urbana-Champaign, Illinois, USA). RNA was prepared and hybridized to the Affymetrix GeneChip Arabidopsis ATH1 Genome Array using the Gene Chip Express Kit (Ambion, Austin, TX, USA).

RESULTS

Tyrosine 831 autophosphorylation of BRI1 regulates Arabidopsis flowering time, and mutation of methionine residues in the extracellular domain of BRI1 affects hypocotyl and root length. BRI1(M656Q)-Flag, BRI1(M657Q)-Flag, and BRI1(M661Q)-Flag seedlings were insensitive to the BL treatment and showed no inhibition of root elongation. However, BRI1(M665Q)-Flag and BRI1(M671Q)-Flag seedlings were sensitive to the BL treatment, and exhibited root elongation inhibition. the early flowering phenotype of BRI1(Y831F)-Flag transgenic plants is consistent with the expression levels of key flowering-related genes, including those promoting flowering (AP1, AP2, and AG) and repressing flowering (FLC and SMZ).

Engineering Chimeras by Fusing Plant Receptor-like Kinase EMS1 and BRI1 Reveals the Two Receptors' Structural Specificity and Molecular Mechanisms

Brassinosteriods (BRs) are plant hormones essential for plant growth and development. The receptor-like kinase (RLK) BRI1 perceives BRs to initiate a well-known transduction pathway which finally activate the transcription factors BZR1/BES1 specifically regulating BR-mediated gene expression. The RLK EMS1 governs tapetum formation via the same signaling pathway shared with BRI1. BRI1 and EMS1 have a common signal output, but the gene structural specificity and the molecular response remain unclear. In this study, we identified that the transmembrane (TM), intracellular juxtamembrane (iJM), kinase, and leucin-rich repeats 1-13 (LRR1-13) domains of EMS1 could replace the corresponding BRI1 domain to maintain the BR receptor function, whereas the extracellular juxtamembrane (eJM) and LRR1-14 domains could not, indicating that the LRR14-EJM domain conferred functional specificity to BRI1. We compared the kinase domains of EMS1 and BRI1, and found that EMS1’s kinase activity was weaker than BRI1’s. Further investigation of the specific phosphorylation sites in BRI1 and EMS1 revealed that the Y1052 site in the kinase domain was essential for the BRI1 biological function, but the corresponding site in EMS1 showed no effect on the biological function of EMS1, suggesting a site regulation difference in the two receptors. Furthermore, we showed that EMS1 shared the substrate BSKs with BRI1. Our study provides insight into the structural specificity and molecular mechanism of BRI1 and EMS1, as well as the origin and divergence of BR receptors.

Phosphorylation of BIK1 is critical for interaction with downstream signaling components

BACKGROUND

Botrytis-induced Kinase 1 (BIK1) is a receptor-like cytoplasmic kinase (RLCK) involved in the defense, growth, and development of higher plants. It interacts with various receptor-like kinases (RLKs) such as Brassinosteroid Insensitive 1 (BRI1), Flagellin Sensitive 2 (FLS2), and Perception of the Arabidopsis Danger Signal Peptide 1 (PEPR1), but little is known about signaling downstream of BIK1.

OBJECTIVE

In this study, we aimed to identify Arabidopsis thaliana BIK1 (AtBIK1) and Brassica rapa BIK1 (BrBIK1) interacting proteins, which is downstream signaling components in Arabidopsis. In addition, the effect of BIK1 phosphorylation on their interaction were examined.

METHODS

For yeast two hybrid (Y2H) screening, a B. rapa cDNA activation domain (AD) library and an A. thaliana cDNA library were used. Reverse reaction (LR) recombinations of appropriate open reading frames (AtBIK1, BrBIK1, AtRGP2, AtPATL2, AtPP7) in either pDONR207 or pDONR/zeo were performed with the split-YFP destination vectors pDEST-GWVYNE and pDEST-GWVYCE to generate N- or C-terminal fusions with the N- and C-terminal yellow fluorescent protein (YFP) moieties, respectively. Recombined vectors were transformed into Agrobacterium strain GV3101. The described GST-AtBIK1, Flag-AtBIK1, and Flag-BrBIK1 constructs were used as templates for site-directed mutagenesis with a QuikChange XL Site-Directed Mutagenesis Kit (Stratagene).

RESULTS

In results, A. thaliana BIK1 (AtBIK1) displays strong autophosphorylation kinase activity on tyrosine and threonine residues, whereas B. rapa BIK1 (BrBIK1) does not exhibit autophosphorylation kinase activity in vitro. Herein, we demonstrated that four proteins (RGP2, PATL2, PP7, and SULTR4.1) interact with BrBIK1 but not AtBIK1 in a Y2H system. To confirm interactions between BIK1 and protein candidates in Nicotiana benthamiana, BiFC analysis was performed and it was found that only BrBIK1 bound the three proteins tested. Three phosphosites, T90, T362, and T368, based on amino acid sequence alignment between AtBIK1 and BrBIK1, and performed site-directed mutagenesis (SDM) on AtBIK1 and BrBIK. S90T, P362T, and A369T mutations in BrBIK1 restored autophosphorylation kinase activity on threonine residues comparable to AtBIK1. However, T90A, T362P, and T368A mutations in AtBIK1 did not alter autophosphorylation kinase activity on threonine residues compared with wild-type AtBIK1. BiFC results showed that BIK1 mutations restored kinase activity led to the loss of the binding activity to RGP2, PATL2, or PP7 proteins.

CONCLUSION

Phospho-BIK1 might be involved in plant innate immunity, while non-phospho BIK1 may regulate plant growth and development through interactions with RGP2, PATL2, and PP7.

Chaperone-like protein DAY plays critical roles in photomorphogenesis

Photomorphogenesis, light-mediated development, is an essential feature of all terrestrial plants. While chloroplast development and brassinosteroid (BR) signaling are known players in photomorphogenesis, proteins that regulate both pathways have yet to be identified. Here we report that DE-ETIOLATION IN THE DARK AND YELLOWING IN THE LIGHT (DAY), a membrane protein containing DnaJ-like domain, plays a dual-role in photomorphogenesis by stabilizing the BR receptor, BRI1, as well as a key enzyme in chlorophyll biosynthesis, POR. DAY localizes to both the endomembrane and chloroplasts via its first transmembrane domain and chloroplast transit peptide, respectively, and interacts with BRI1 and POR in their respective subcellular compartments. Using genetic analysis, we show that DAY acts independently on BR signaling and chlorophyll biogenesis. Collectively, this work uncovers DAY as a factor that simultaneously regulates BR signaling and chloroplast development, revealing a key regulator of photomorphogenesis that acts across cell compartments.

Brassinosteroids synthesised by CYP85A/A1 but not CYP85A2 function via a BRI1-like receptor but not via BRI1 in Picea abies

Brassinosteroids (BRs) are essential plant hormones. In angiosperms, brassinolide and castasterone, the first and second most active BRs, respectively, are synthesised by CYP85A2 and CYP85A/A1, respectively. BRs in angiosperms function through an essential receptor, BR Insensitive 1 (BRI1). In addition, some angiosperms also have non-essential BRI1-like 1/3 (BRL1/3). In conifers, BRs promote seed germination under drought stress; however, how BRs function in gymnosperms is unknown. In this study, we performed functional complementation of BR biosynthesis and receptor genes from Picea abies with respective Arabidopsis mutants. We found that P. abies possessed functional PaCYP85A and PaBRL1 but not PaCYP85A2 or PaBRI1, and this results in weak BR signaling, and both PaCYP85A and PaBRL1 were abundantly expressed. However, neither BR treatment of P. abies seedlings nor expression of PaBRL1 in the Arabidopsis Atbri1 mutant promoted plant height, despite the fact that BR-responsive genes were activated. Importantly, chimeric AtBRI1 replaced with the BR-binding domain of PaBRL1 complemented the Atbri1 phenotypes. Furthermore, PaBRL1 had less kinase activity than BRI1 in vitro. Overall, P. abies had weak but still active BR signaling, explaining aspects of its slow growth and high stress tolerance. Our study sheds light on the functional and evolutionary significance of distinct BR signaling that is independent of BRI1 and brassinolide.

Moonlighting Proteins Shine New Light on Molecular Signaling Niches

Plants as sessile organisms face daily environmental challenges and have developed highly nuanced signaling systems to enable suitable growth, development, defense, or stalling responses. Moonlighting proteins have multiple tasks and contribute to cellular signaling cascades where they produce additional variables adding to the complexity or fuzziness of biological systems. Here we examine roles of moonlighting kinases that also generate 3',5'-cyclic guanosine monophosphate (cGMP) in plants. These proteins include receptor like kinases and lipid kinases. Their guanylate cyclase activity potentiates the development of localized cGMP-enriched nanodomains or niches surrounding the kinase and its interactome. These nanodomains contribute to allosteric regulation of kinase and other molecules in the immediate complex directly or indirectly modulating signal cascades. Effects include downregulation of kinase activity, modulation of other members of the protein complexes such as cyclic nucleotide gated channels and potential triggering of cGMP-dependent degradation cascades terminating signaling. The additional layers of information provided by the moonlighting kinases are discussed in terms of how they may be used to provide a layer of fuzziness to effectively modulate cellular signaling cascades.

Barley "uzu" and Wheat "uzu-like" Brassinosteroid Receptor BRI1 Kinase Domain Variations Modify Phosphorylation Activity In Vitro

Brassinosteroid insensitive1 (BRI1), a leucine-rich repeat receptor kinase, is responsible for the perception of the brassinosteroid (BR) phytohormone in plants. While recent evidence has implicated a naturally occurring Hordeum vulgare V. (barley) HvBRI1 kinase domain (KD) variant (H857R; "uzu" variation) in increased fungal disease resistance, the impact of the variation on receptor function and thus the mechanism by which disease resistance might be imparted remain enigmatic. Here, the functional implications of the uzu variation as well as the effects of newly identified naturally occurring Triticum aestivum L. (wheat) TaBRI1-KD variants are investigated. Recombinantly produced KDs of wild-type (WT) and uzu HvBRI1 were assessed for phosphorylation activity in vitro, yielding WT K_M and V_MAX values similar to those of other reports, but the uzu variation delayed saturation and reduced turnover levels. In silico modeling of the H857R variation showed it to be surface-exposed and distal from the catalytic site. Further evaluation of three naturally occurring wheat TaBRI1 variants, A907T, A970V, and G1019R (barley numbering) identified in the A, B, and D subgenomic genes, respectively, highlighted a significant loss of activity for A907T. A907T is located on the same surface as the H857R variation and a negative regulatory phosphorylation site (T982) in Arabidopsis thaliana BRI1. A fourth variation, T1031A (barley numbering), unique to both subgenomic A proteins and localized to the BKI1 binding site, also decreased activity. The outcomes are discussed with respect to the predicted structural contexts of the variations and their implications with respect to mechanisms of action.

Regulation of Three Key Kinases of Brassinosteroid Signaling Pathway

Brassinosteroids (BRs) are important plant growth hormones that regulate a wide range of plant growth and developmental processes. The BR signals are perceived by two cell surface-localized receptor kinases, Brassinosteroid-Insensitive1 (BRI1) and BRI1-Associated receptor Kinase (BAK1), and reach the nucleus through two master transcription factors, bri1-EMS suppressor1 (BES1) and Brassinazole-resistant1 (BZR1). The intracellular transmission of the BR signals from BRI1/BAK1 to BES1/BZR1 is inhibited by a constitutively active kinase Brassinosteroid-Insensitive2 (BIN2) that phosphorylates and negatively regulates BES1/BZR1. Since their initial discoveries, further studies have revealed a plethora of biochemical and cellular mechanisms that regulate their protein abundance, subcellular localizations, and signaling activities. In this review, we provide a critical analysis of the current literature concerning activation, inactivation, and other regulatory mechanisms of three key kinases of the BR signaling cascade, BRI1, BAK1, and BIN2, and discuss some unresolved controversies and outstanding questions that require further investigation.

Emerging roles of vascular brassinosteroid receptors of the BRI1-like family

Brassinosteroids (BRs) are essential hormones for plant growth and development that are perceived at the plasma membrane by a group of Leucine-Rich Repeat Receptor-Like Kinases (LRR-RLKs) of the BRASSINOSTEROID INSENSITIVE 1 (BRI1) family. The BRI1 receptor was first discovered by genetic screenings based on the dwarfism of BR-deficient plants. There are three BRI1 homologs, named BRI1-like 1, 2 and 3 (BRLs), yet only BRL1 and BRL3 behave as functional BR receptors. Whereas the BRI1 pathway operates in the majority of cells to promote growth, BRL receptor signaling operates under specific spatiotemporal constraints. Despite a wealth of information on the BRI1 pathway, data on specific BRL pathways and their biological relevance is just starting to emerge. Here, we systematically compare BRLs with BRI1 to identify any differences that could account for specific receptor functions. Understanding how vascular and cell-specific BRL receptors orchestrate plant development and adaptation to the environment will help shed light on membrane signaling and cell communication in plants, while opening up novel possibilities to improve stress adaptation without penalizing growth.

Biochemical Analysis of the Role of Leucine-Rich Repeat Receptor-Like Kinases and the Carboxy-Terminus of Receptor Kinases in Regulating Kinase Activity in Arabidopsis thaliana and Brassica oleracea

Protein post-translational modification by phosphorylation is essential for the activity and stability of proteins in higher plants and underlies their responses to diverse stimuli. There are more than 300 leucine-rich repeat receptor-like kinases (LRR-RLKs), a major group of receptor-like kinases (RLKs) that plays an important role in growth, development, and biotic stress responses in higher plants. To analyze auto- and transphosphorylation patterns and kinase activities in vitro, 43 full-length complementary DNA (cDNA) sequences were cloned from genes encoding LRR-RLKs. Autophosphorylation activity was found in the cytoplasmic domains (CDs) of 18 LRR-RLKs; 13 of these LRR-RLKs with autophosphorylation activity showed transphosphorylation in Escherichia coli. BRI1-Associated Receptor Kinase (BAK1), which is critically involved in the brassinosteroid and plant innate immunity signal transduction pathways, showed strong auto- and transphosphorylation with multi-specific kinase activity within 2 h of induction of Brassica oleraceae BAK1-CD (BoBAK1-CD) in E. coli; moreover, the carboxy-terminus of LRR-RLKs regulated phosphorylation and kinase activity in Arabidopsis thaliana and vegetative crops.

The brassinosteroid receptor BRI1 can generate cGMP enabling cGMP-dependent downstream signaling

The brassinosteroid receptor brassinosteroid insensitive 1 (BRI1) is a member of the leucine-rich repeat receptor-like kinase family. The intracellular kinase domain of BRI1 is an active kinase and also encapsulates a guanylate cyclase catalytic centre. Using liquid chromatography tandem mass spectrometry, we confirmed that the recombinant cytoplasmic domain of BRI1 generates pmol amounts of cGMP per μg protein with a preference for magnesium over manganese as a co-factor. Importantly, a functional BRI1 kinase is essential for optimal cGMP generation. Therefore, the guanylate cyclase activity of BRI1 is modulated by the kinase while cGMP, the product of the guanylate cyclase, in turn inhibits BRI1 kinase activity. Furthermore, we show using Arabidopsis root cell cultures that cGMP rapidly potentiates phosphorylation of the downstream substrate brassinosteroid signaling kinase 1 (BSK1). Taken together, our results suggest that cGMP acts as a modulator that enhances downstream signaling while dampening signal generation from the receptor.

Scanning for New BRI1 Mutations via TILLING Analysis

The identification and characterization of a mutational spectrum for a specific protein can help to elucidate its detailed cellular functions. BRASSINOSTEROID INSENSITIVE1 (BRI1), a multidomain transmembrane receptor-like kinase, is a major receptor of brassinosteroids in Arabidopsis (Arabidopsis thaliana). Within the last two decades, over 20 different bri1 mutant alleles have been identified, which helped to determine the significance of each domain within BRI1. To further understand the molecular mechanisms of BRI1, we tried to identify additional alleles via targeted induced local lesions in genomes. Here, we report our identification of 83 new point mutations in BRI1, including nine mutations that exhibit an allelic series of typical bri1 phenotypes, from subtle to severe morphological alterations. We carried out biochemical analyses to investigate possible mechanisms of these mutations in affecting brassinosteroid signaling. A number of interesting mutations have been isolated via this study. For example, bri1-702, the only weak allele identified so far with a mutation in the activation loop, showed reduced autophosphorylation activity. bri1-705, a subtle allele with a mutation in the extracellular portion, disrupts the interaction of BRI1 with its ligand brassinolide and coreceptor BRI1-ASSOCIATED RECEPTOR KINASE1. bri1-706, with a mutation in the extracellular portion, is a subtle defective mutant. Surprisingly, root inhibition analysis indicated that it is largely insensitive to exogenous brassinolide treatment. In this study, we found that bri1-301 possesses kinase activity in vivo, clarifying a previous report arguing that kinase activity may not be necessary for the function of BRI1. These data provide additional insights into our understanding of the early events in the brassinosteroid signaling pathway.

Plant cell wall signalling and receptor-like kinases

Communication between the extracellular matrix and the cell interior is essential for all organisms as intrinsic and extrinsic cues have to be integrated to co-ordinate development, growth, and behaviour. This applies in particular to plants, the growth and shape of which is governed by deposition and remodelling of the cell wall, a rigid, yet dynamic, extracellular network. It is thus generally assumed that cell wall surveillance pathways exist to monitor the state of the wall and, if needed, elicit compensatory responses such as altered expression of cell wall remodelling and biosynthesis genes. Here, I highlight recent advances in the field of cell wall signalling in plants, with emphasis on the role of plasma membrane receptor-like kinase complexes. In addition, possible roles for cell wall-mediated signalling beyond the maintenance of cell wall integrity are discussed.

Expression of Plant Receptor Kinases in E. coli

Plant receptor kinases play diverse signaling roles in disease resistance and plant development. They represent a large plant gene family with over 600 members in Arabidopsis thaliana. While the functions of several members of the receptor kinase family have now been elucidated, a great proportion still remains uncharacterized. The structural and functional characterization of such plant receptor kinases may entail biochemical approaches that require access to purified protein, which can be made possible through heterologous protein expression. This chapter describes a strategy for expressing plant receptor kinases in E. coli, a bacterial host that has successfully been used to express and purify certain plant receptor kinase domains, some of which were subsequently used for biochemical assays. As full-length receptor-like kinases may be difficult to express, it is suggested to clone and express domains separately, after having identified domain borders using bioinformatics tools. A detailed cloning protocol is provided, as well as advice for testing expression efficiency and handling of expressed protein ending up in inclusion bodies.

Activation of the LRR Receptor-Like Kinase PSY1R Requires Transphosphorylation of Residues in the Activation Loop

PSY1R is a leucine-rich repeat (LRR) receptor-like kinase (RLK) previously shown to act as receptor for the plant peptide hormone PSY1 (peptide containing sulfated tyrosine 1) and to regulate cell expansion. PSY1R phosphorylates and thereby regulates the activity of plasma membrane-localized H⁺-ATPases. While this mechanism has been studied in detail, little is known about how PSY1R itself is activated. Here we studied the activation mechanism of PSY1R. We show that full-length PSY1R interacts with members of the SERK co-receptor family in planta. We identified seven in vitro autophosphorylation sites on serine and threonine residues within the kinase domain of PSY1R using mass spectrometry. We furthermore show that PSY1R autophosphorylation occurs in trans and that the initial transphosphorylation takes place within the activation loop at residues Ser951, Thr959, and Thr963. While Thr959 and Thr963 are conserved among other related plant LRR RLKs, Ser951 is unique to PSY1R. Based on homology modeling we propose that phosphorylation of Ser951 stabilize the inactive conformation of PSY1R.

A Quantitative Proteomic Analysis of Brassinosteroid-induced Protein Phosphorylation in Rice (Oryza sativa L.)

The group of polyhydroxysteroid phytohormones referred to as the brassinosteroids (BRs) is known to act on plant development and the stress response. BR signal transduction relies largely on protein phosphorylation. By employing a label-free, MS (Mass Spectrometry)-based phosphoproteomic approach, we report here the largest profiling of 4,034 phosphosites on 1,900 phosphoproteins from rice young seedlings and their dynamic response to BR. 1,821 proteins, including kinases, transcription factors and core components of BR and other hormone signaling pathways, were found to be differentially phosphorylated during the BR treatment. A Western blot analysis verified the differential phosphorylation of five of these proteins, implying that the MS-based phosphoproteomic data were robust. It is proposed that the dephosphorylation of gibberellin (GA) signaling components could represent an important mechanism for the BR-regulated antagonism to GA, and that BR influences the plant architecture of rice by regulating cellulose synthesis via phosphorylation.

Autophosphorylation of Specific Threonine and Tyrosine Residues in Arabidopsis CERK1 is Essential for the Activation of Chitin-Induced Immune Signaling

Pattern recognition receptors on the plant cell surface mediate the recognition of microbe/damage-associated molecular patterns (MAMPs/DAMPs) and activate downstream immune signaling. Autophosphorylation of signaling receptor-like kinases is a critical event for the activation of downstream responses but the function of each phosphorylation site in the regulation of immune signaling is not well understood. In this study, 41 Ser/Thr/Tyr and 15 Ser/Thr residues were identified as in vitro and in vivo autophosphorylation sites of Arabidopsis CERK1, which is essential for chitin signaling. Comprehensive analysis of transgenic plants expressing mutated CERK1 genes for each phosphorylation site in the cerk1-2 background indicated that the phosphorylation of T479 in the activation segment and Y428 located upstream of the catalytic loop is important for the activation of chitin-triggered defense responses. Contribution of the phosphorylation of T573 to the chitin responses was also suggested. In vitro evaluation of kinase activities of mutated kinase domains indicated that the phosphorylation of T479 and T573 is directly involved in the regulation of kinase activity of CERK1 but the phosphorylation of Y428 regulates chitin signaling independently of the regulation of kinase activity. These results indicated that the phosphorylation of specific residues in the kinase domain contributes to the regulation of downstream signaling either through the regulation of kinase activity or the different mechanisms, e.g. regulation of protein-protein interactions.

OsREM4.1 Interacts with OsSERK1 to Coordinate the Interlinking between Abscisic Acid and Brassinosteroid Signaling in Rice

Crosstalk among phytohormones is crucial for balancing plant growth and adjustment to various environments. Abscisic acid (ABA) and brassinosteroids (BRs) exhibit antagonistic interactions during many plant development processes, but little is known about the molecular mechanism mediating those interactions. Here, we identified a rice (Oryza sativa) remorin gene, OsREM4.1, whose expression is upregulated by ABA through the transcriptional activator OsbZIP23. OsREM4.1, in return, negatively regulates BR signaling output. We discovered that OsREM4.1 interacts with OsSERK1 to inhibit its interaction with rice BR receptor OsBRI1. Moreover, OsBRI1 could phosphorylate OsREM4.1 to reduce the binding affinity of OsREM4.1 to OsSERK1. These results demonstrate that OsREM4.1 is transcriptionally regulated by ABA and functions as an OsBRI1 substrate and OsSERK1-interacting protein to inhibit the formation and subsequent activation of the OsBRI1-OsSERK1 receptor complex. Our findings provide insight into the mechanism by which the antagonistic interactions between ABA and BRs are coordinated in rice.

Analysis of Phosphorylation of the Receptor-Like Protein Kinase HAESA during Arabidopsis Floral Abscission

Receptor-like protein kinases (RLKs) are the largest family of plant transmembrane signaling proteins. Here we present functional analysis of HAESA, an RLK that regulates floral organ abscission in Arabidopsis. Through in vitro and in vivo analysis of HAE phosphorylation, we provide evidence that a conserved phosphorylation site on a region of the HAE protein kinase domain known as the activation segment positively regulates HAE activity. Additional analysis has identified another putative activation segment phosphorylation site common to multiple RLKs that potentially modulates HAE activity. Comparative analysis suggests that phosphorylation of this second activation segment residue is an RLK specific adaptation that may regulate protein kinase activity and substrate specificity. A growing number of RLKs have been shown to exhibit biologically relevant dual specificity toward serine/threonine and tyrosine residues, but the mechanisms underlying dual specificity of RLKs are not well understood. We show that a phospho-mimetic mutant of both HAE activation segment residues exhibits enhanced tyrosine auto-phosphorylation in vitro, indicating phosphorylation of this residue may contribute to dual specificity of HAE. These results add to an emerging framework for understanding the mechanisms and evolution of regulation of RLK activity and substrate specificity.

Conserved phosphorylation sites in the activation loop of the Arabidopsis phytosulfokine receptor PSKR1 differentially affect kinase and receptor activity

Phytosulfokine is perceived by a leucine-rich repeat receptor-like kinase with auto- and trans-phosphorylation activity. Phosphosite mapping indicated that multisite serine/threonine autophosphorylation probably occurs within the activation loop of the kinase. Phosphoablative mutations differentially impair kinase activity in vitro and receptor function in planta.

PSK (phytosulfokine) is a plant peptide hormone perceived by a leucine-rich repeat receptor kinase. Phosphosite mapping of epitope-tagged PSKR1 (phytosulfokine receptor 1) from Arabidopsis thaliana plants identified Ser⁶⁹⁶ and Ser⁶⁹⁸ in the JM (juxtamembrane) region and probably Ser⁸⁸⁶ and/or Ser⁸⁹³ in the AL (activation loop) as in planta phosphorylation sites. In vitro-expressed kinase was autophosphorylated at Ser⁷¹⁷ in the JM, and at Ser⁷³³, Thr⁷⁵², Ser⁷⁸³, Ser⁸⁶⁴, Ser⁹¹¹, Ser⁹⁵⁸ and Thr⁹⁹⁸ in the kinase domain. The LC–ESI–MS/MS spectra provided support that up to three sites (Thr⁸⁹⁰, Ser⁸⁹³ and Thr⁸⁹⁴) in the AL were likely to be phosphorylated in vitro. These sites are evolutionarily highly conserved in PSK receptors, indicative of a conserved function. Site-directed mutagenesis of the four conserved residues in the activation segment, Thr⁸⁹⁰, Ser⁸⁹³, Thr⁸⁹⁴ and Thr⁸⁹⁹, differentially altered kinase activity in vitro and growth-promoting activity in planta. The T899A and the quadruple-mutated TSTT-A (T890A/S893A/T894A/T899A) mutants were both kinase-inactive, but PSKR1(T899A) retained growth-promoting activity. The T890A and S893A/T894A substitutions diminished kinase activity and growth promotion. We hypothesize that phosphorylation within the AL activates kinase activity and receptor function in a gradual and distinctive manner that may be a means to modulate the PSK response.

MicroProteins: small size-big impact

MicroProteins (miPs) are short, usually single-domain proteins that, in analogy to miRNAs, heterodimerize with their targets and exert a dominant-negative effect. Recent bioinformatic attempts to identify miPs have resulted in a list of potential miPs, many of which lack the defining characteristics of a miP. In this opinion article, we clearly state the characteristics of a miP as evidenced by known proteins that fit the definition; we explain why modulatory proteins misrepresented as miPs do not qualify as true miPs. We also discuss the evolutionary history of miPs, and how the miP concept can extend beyond transcription factors (TFs) to encompass different non-TF proteins that require dimerization for full function.

Functional analysis of the BRI1 receptor kinase by Thr-for-Ser substitution in a regulatory autophosphorylation site

BRI1 becomes highly phosphorylated in vivo upon perception of the ligand, brassinolide, as a result of autophosphorylation and transphosphorylation by its co-receptor kinase, BAK1. Important autophosphorylation sites include those involved in activation of kinase activity and those that are inhibitory, such as Ser-891. The inhibitory sites are autophosphorylated after kinase activation has been achieved and are postulated to contribute to deactivation of the kinase. The function of phosphosites is usually tested by substituting a non-phosphorylatable residue or an acidic residue that can act as a phosphomimetic. What has typically not been examined is substitution of a Thr for a Ser phosphosite (or vice versa) but given that Thr and Ser are not equivalent amino acids this type of substitution may represent a new approach to engineer regulatory phosphorylation. In the present study with BRI1, we substituted Thr at the Ser-891 phosphosite to generate the S891T directed mutant. The recombinant Flag-BRI1 (S891T) cytoplasmic domain protein (the S891T protein) was catalytically active and phosphorylation occurred at the engineered Thr-891 site. However, the S891T recombinant protein autophosphorylated more slowly than the wild-type protein during expression in E. coli. As a result, activation of peptide kinase activity (measured in vitro) was delayed as was transphosphorylation of bacterial proteins in situ. Stable transgenic expression of BRI1 (S891T)-Flag in Arabidopsis bri1-5 plants did not fully rescue the brassinosteroid (BR) phenotype indicating that BR signaling was constrained. Our working model is that restricted signaling in the S891T plants occurs as a result of the reduced rate of activation of the mutant BRI1 kinase by autophosphorylation. These results provide the platform for future studies to critically test this new model in vivo and establish Ser-Thr substitutions at phosphosites as an interesting approach to consider with other protein kinases.

An autophosphorylation site database for leucine-rich repeat receptor-like kinases in Arabidopsis thaliana

Leucine-rich repeat receptor-like kinases (LRR RLKs) form a large family of plant signaling proteins consisting of an extracellular domain connected by a single-pass transmembrane sequence to a cytoplasmic kinase domain. Autophosphorylation on specific Ser and/or Thr residues in the cytoplasmic domain is often critical for the activation of several LRR RLK family members with proven functional roles in plant growth regulation, morphogenesis, disease resistance, and stress responses. While identification and functional characterization of in vivo phosphorylation sites is ultimately required for a full understanding of LRR RLK biology and function, bacterial expression of recombinant LRR RLK cytoplasmic catalytic domains for identification of in vitro autophosphorylation sites provides a useful resource for further targeted identification and functional analysis of in vivo sites. In this study we employed high-throughput cloning and a variety of mass spectrometry approaches to generate an autophosphorylation site database representative of more than 30% of the approximately 223 LRR RLKs in Arabidopsis thaliana. We used His-tagged constructs of complete cytoplasmic domains to identify a total of 592 phosphorylation events across 73 LRR RLKs, with 497 sites uniquely assigned to specific Ser (268 sites) or Thr (229 sites) residues in 68 LRR RLKs. Multiple autophosphorylation sites per LRR RLK were the norm, with an average of seven sites per cytoplasmic domain, while some proteins showed more than 20 unique autophosphorylation sites. The database was used to analyze trends in the localization of phosphorylation sites across cytoplasmic kinase subdomains and to derive a statistically significant sequence motif for phospho-Ser autophosphorylation.

Glutaredoxin AtGRXC2 catalyses inhibitory glutathionylation of Arabidopsis BRI1-associated receptor-like kinase 1 (BAK1) in vitro

Reversible protein phosphorylation, catalysed by protein kinases, is the most widely studied post-translational modification (PTM), whereas the analysis of other modifications such as S-thiolation is in its relative infancy. In a yeast-two-hybrid (Y2H) screen, we identified a number of novel putative brassinosteroid insensitive 1 (BR1)-associated receptor-like kinase 1 (BAK1) interacting proteins including several proteins related to redox regulation. Glutaredoxin (GRX) C2 (AtGRXC2) was among candidate proteins identified in the Y2H screen and its interaction with recombinant Flag–BAK1 cytoplasmic domain was confirmed using an in vitro pull-down approach. We show that BAK1 peptide kinase activity is sensitive to the oxidizing agents H2O2 and diamide in vitro, suggesting that cysteine oxidation might contribute to control of BAK1 activity. Furthermore, BAK1 was glutathionylated and this reaction could occur via a thiolate-dependent reaction with GSSG or a H2O2-dependent reaction with GSH and inhibited kinase activity. Surprisingly, both reactions were catalysed by AtGRXC2 at lower concentrations of GSSG or GSH than reacted non-enzymatically. Using MALDI–TOF MS, we identified Cys353, Cys374 and Cys408 as potential sites of glutathionylation on the BAK1 cytoplasmic domain and directed mutagenesis suggests that Cys353 and Cys408 are major sites of GRXC2-mediated glutathionylation. Collectively, these results highlight the potential for redox control of BAK1 and demonstrate the ability of AtGRXC2 to catalyse protein glutathionylation, a function not previously described for any plant GRX. The present work presents a foundation for future studies of glutathionylation of plant receptor-like protein kinases (RLKs) as well as for the analysis of activities of plant GRXs.

The E3 ligase OsPUB15 interacts with the receptor-like kinase PID2 and regulates plant cell death and innate immunity

BACKGROUND

Rice blast disease is one of the most destructive diseases of rice worldwide. We previously cloned the rice blast resistance gene Pid2, which encodes a transmembrane receptor-like kinase containing an extracellular B-lectin domain and an intracellular serine/threonine kinase domain. However, little is known about Pid2-mediated signaling.

RESULTS

Here we report the functional characterization of the U-box/ARM repeat protein OsPUB15 as one of the PID2-binding proteins. We found that OsPUB15 physically interacted with the kinase domain of PID2 (PID2K) in vitro and in vivo and the ARM repeat domain of OsPUB15 was essential for the interaction. In vitro biochemical assays indicated that PID2K possessed kinase activity and was able to phosphorylate OsPUB15. We also found that the phosphorylated form of OsPUB15 possessed E3 ligase activity. Expression pattern analyses revealed that OsPUB15 was constitutively expressed and its encoded protein OsPUB15 was localized in cytosol. Transgenic rice plants over-expressing OsPUB15 at early stage displayed cell death lesions spontaneously in association with a constitutive activation of plant basal defense responses, including excessive accumulation of hydrogen peroxide, up-regulated expression of pathogenesis-related genes and enhanced resistance to blast strains. We also observed that, along with plant growth, the cell death lesions kept spreading over the whole seedlings quickly resulting in a seedling lethal phenotype.

CONCLUSIONS

These results reveal that the E3 ligase OsPUB15 interacts directly with the receptor-like kinase PID2 and regulates plant cell death and blast disease resistance.

Molecular dissection of the response of a rice leucine-rich repeat receptor-like kinase (LRR-RLK) gene to abiotic stresses

Leucine-rich repeat (LRR) receptor-like kinase (RLK) proteins play key roles in a variety of biological pathways. In a previous study, we analyzed the members of the rice LRR-RLK gene family using in silico analysis. A total of 23 LRR-RLK genes were selected based on the expression patterns of a genome-wide dataset of microarrays. The Oryza sativa gamma-ray induced LRR-RLK1 (OsGIRL1) gene was highly induced by gamma irradiation. Therefore, we studied its expression pattern in response to various different abiotic and phytohormone treatments. OsGIRL1 was induced on exposure to abiotic stresses such as salt, osmotic, and heat, salicylic acid (SA), and abscisic acid (ABA), but exhibited downregulation in response to jasmonic acid (JA) treatment. The OsGIRL1 protein was clearly localized at the plasma membrane. The truncated proteins harboring juxtamembrane and kinase domains (or only harboring a kinase domain) exhibited strong autophosphorylation. The biological function of OsGIRL1 was investigated via heterologous overexpression of this gene in Arabidopsis plants subjected to gamma-ray irradiation, salt stress, osmotic stress, and heat stress. A hypersensitive response was observed in response to salt stress and heat stress, whereas a hyposensitive response was observed in response to gamma-ray treatment and osmotic stress. These results provide critical insights into the molecular functions of the rice LRR-RLK genes as receptors of external signals.

Structural insights into the negative regulation of BRI1 signaling by BRI1-interacting protein BKI1

Brassinosteroids (BRs) are essential steroid hormones that have crucial roles in plant growth and development. BRs are perceived by the cell-surface receptor-like kinase brassinosteroid insensitive 1 (BRI1). In the absence of BRs, the cytosolic kinase domain (KD) of BRI1 is inhibited by its auto-inhibitory carboxyl terminus, as well as by interacting with an inhibitor protein, BRI1 kinase inhibitor 1 (BKI1). How BR binding to the extracellular domain of BRI1 leads to activation of the KD and dissociation of BKI1 into the cytosol remains unclear. Here we report the crystal structure of BRI1 KD in complex with the interacting peptide derived from BKI1. We also provide biochemical evidence that BRI1-associated kinase 1 (BAK1) plays an essential role in initiating BR signaling. Steroid-dependent heterodimerization of BRI1 and BAK1 ectodomains brings their cytoplasmic KDs in the right orientation for competing with BKI1 and transphosphorylation.

Distinct signaling mechanisms in multiple developmental pathways by the SCRAMBLED receptor of Arabidopsis

SCRAMBLED (SCM), a leucine-rich repeat receptor-like kinase in Arabidopsis (Arabidopsis thaliana), is required for positional signaling in the root epidermis and for tissue/organ development in the shoot. To further understand SCM action, we generated a series of kinase domain variants and analyzed their ability to complement scm mutant defects. We found that the SCM kinase domain, but not kinase activity, is required for its role in root epidermal patterning, supporting the view that SCM is an atypical receptor kinase. We also describe a previously uncharacterized role for SCM in fruit dehiscence, because mature siliques from scm mutants fail to open properly. Interestingly, the kinase domain of SCM appears to be dispensable for this developmental process. Furthermore, we found that most of the SCM kinase domain mutations dramatically inhibit inflorescence development. Because this process is not affected in scm null mutants, it is likely that SCM acts redundantly to regulate inflorescence size. The importance of distinct kinase residues for these three developmental processes provides an explanation for the maintenance of the conserved kinase domain in the SCM protein, and it may generally explain its conservation in other atypical kinases. Furthermore, these results indicate that individual leucine-rich repeat receptor-like kinases may participate in multiple pathways using distinct signaling mechanisms to mediate diverse cellular communication events.

Gatekeeper tyrosine phosphorylation is autoinhibitory for Symbiosis Receptor Kinase

Plant receptor-like kinases (RLKs) are distinguished by having a tyrosine in the 'gatekeeper' position. Previously we reported Symbiosis Receptor Kinase from Arachis hypogaea (AhSYMRK) to autophosphorylate on the gatekeeper tyrosine (Y670), though this phosphorylation was not necessary for the kinase activity. Here we report that recombinant catalytic domain of AhSYMRK with a phosphomimic substitution in the gatekeeper position (Y670E) is catalytically almost inactive and is conformationally quite distinct from the corresponding native enzyme. Additionally, we show that gatekeeper-phosphorylated AhSYMRK polypeptides are inactive and depletion of this inactive form leads to activation of intramolecular autophosphorylation of AhSYMRK. Together, our results suggest gatekeeper tyrosine autophosphorylation to be autoinhibitory for AhSYMRK.

Assessment of BAK1 activity in different plant receptor-like kinase complexes by quantitative profiling of phosphorylation patterns

Plant receptor-like kinases (RLKs) constitute a large family of receptors coordinating developmental programs with adaptation to environmental stresses including immune defenses. BRI1-ASSOCIATED KINASE 1 (BAK1), a member of the plant RLK family, forms receptor complexes with multiple RLK proteins including BRI1, FLS2, EFR and BIK1 to regulate responses to growth hormones or PAMPs. RLK activation and signal initiation involve protein complex formation and phosphorylation/dephosphorylation between BAK1 and its interacting partners. To gain new insight into how phosphorylation contributes to BAK1-mediated signaling specificity, we first mapped the phosphorylation patterns of BAK1 associated with different RLK partners (BRI1, FLS2, EFR and BIK1). Quantitative phospho-pattern profiling by label-free mass spectrometry revealed that differential phosphorylation patterns of RLK partners resulted from altered BAK1 phosphorylation status. More interestingly, the study of two BAK1 mutants (T450A and C408Y) both showing severe defect in immune defense yet normal growth phenotype suggested that varied phosphorylation patterns of RLK partners by BAK1 could be the molecular basis for selective regulation of multiple BAK1-dependent pathways. Taken together, this phospho-pattern profiling strategy allowed for explicit assessment of BAK1 kinase activity in different RLK complexes, which would facilitate elucidation of BAK1 diverse functions in plant development, defense, and adaptation.

BIOLOGICAL SIGNIFICANCE

BAK1 is a functionally important co-receptor known to interact with different receptor-like kinases (RLKs) to coordinate plant development and immune defenses. Our study first mapped the phosphorylation patterns of BAK1 associated with four RLK partners (BRI1, FLS2, EFR and BIK1), and further revealed that differential phosphorylation patterns of multiple RLK partners resulted from altered BAK1 phosphorylation status. More interestingly, the study of two BAK1 mutants suggested that varied phosphorylation patterns of RLK partners by BAK1 could be the basis for selective regulation of signaling pathways. Taken together, this phospho-pattern profiling strategy allowed for explicit assessment of BAK1 kinase activity in different RLK complexes, which would facilitate elucidation of BAK1 diverse functions in plant development, defense, and adaptation.

Kinase activity and calmodulin binding are essential for growth signaling by the phytosulfokine receptor PSKR1

The cell growth-promoting peptide phytosulfokine (PSK) is perceived by leucine-rich repeat (LRR) receptor kinases. To elucidate PSK receptor function we analyzed PSKR1 kinase activity and binding to Ca(2+) sensors and evaluated the contribution of these activities to growth control in planta. Ectopically expressed PSKR1 was capable of auto- and transphosphorylation. Replacement of a conserved lysine within the ATP-binding region by a glutamate resulted in the inhibition of auto- and transphosphorylation kinase activities. Expression of the kinase-inactive PSKR1(K762E) receptor in the pskr null background did not restore root or shoot growth. Instead, the mutant phenotype was enhanced suggesting that the inactive receptor protein exerts growth-inhibitory activity. Bioinformatic analysis predicted a putative calmodulin (CaM)-binding site within PSKR1 kinase subdomain VIa. Bimolecular fluorescence complementation analysis demonstrated that PSKR1 binds to all isoforms of CaM, more weakly to the CaM-like protein CML8 but apparently not to CML9. Mutation of a conserved tryptophan (W831S) within the predicted CaM-binding site strongly reduced CaM binding. Expression of PSKR1(W831S) in the pskr null background resulted in growth inhibition that was similar to that of the kinase-inactive receptor. We conclude that PSK signaling requires Ca(2+) /CaM binding and kinase activity of PSKR1 in planta. We further propose that the inactivated kinase interferes with other growth-promoting signaling pathway(s).

Crystal structures of the phosphorylated BRI1 kinase domain and implications for brassinosteroid signal initiation

Brassinosteroids, which control plant growth and development, are sensed by the membrane receptor kinase BRASSINOSTEROID INSENSITIVE 1 (BRI1). Brassinosteroid binding to the BRI1 leucine-rich repeat (LRR) domain induces heteromerisation with a SOMATIC EMBRYOGENESIS RECEPTOR KINASE (SERK)-family co-receptor. This process allows the cytoplasmic kinase domains of BRI1 and SERK to interact, trans-phosphorylate and activate each other. Here we report crystal structures of the BRI1 kinase domain in its activated form and in complex with nucleotides. BRI1 has structural features reminiscent of both serine/threonine and tyrosine kinases, providing insight into the evolution of dual-specificity kinases in plants. Phosphorylation of Thr1039, Ser1042 and Ser1044 causes formation of a catalytically competent activation loop. Mapping previously identified serine/threonine and tyrosine phosphorylation sites onto the structure, we analyse their contribution to brassinosteroid signaling. The location of known genetic missense alleles provide detailed insight into the BRI1 kinase mechanism, while our analyses are inconsistent with a previously reported guanylate cyclase activity. We identify a protein interaction surface on the C-terminal lobe of the kinase and demonstrate that the isolated BRI1, SERK2 and SERK3 cytoplasmic segments form homodimers in solution and have a weak tendency to heteromerise. We propose a model in which heterodimerisation of the BRI1 and SERK ectodomains brings their cytoplasmic kinase domains in a catalytically competent arrangement, an interaction that can be modulated by the BRI1 inhibitor protein BKI1.

The Carboxy-terminus of BAK1 regulates kinase activity and is required for normal growth of Arabidopsis

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.

Ligand perception, activation, and early signaling of plant steroid receptor brassinosteroid insensitive 1

Leucine-rich repeat receptor-like kinases (LRR-RLKs) belong to a large group of cell surface proteins involved in many aspects of plant development and environmental responses in both monocots and dicots. Brassinosteroid insensitive 1 (BRI1), a member of the LRR X subfamily, was first identified through several forward genetic screenings for mutants insensitive to brassinosteroids (BRs), which are a class of plant-specific steroid hormones. Since its identification, BRI1 and its homologs had been proved as receptors perceiving BRs and initiating BR signaling. The co-receptor BRI1-associated kinase 1 and its homologs, and other BRI1 interacting proteins such as its inhibitor BRI1 kinase inhibitor 1 (BKI1) were identified by genetic and biochemical approaches. The detailed mechanisms of BR perception by BRI1 and the activation of BRI1 receptor complex have also been elucidated. Moreover, several mechanisms for termination of the activated BRI1 signaling were also discovered. In this review, we will focus on the recent advances on the mechanism of BRI1 phosphorylation and activation, the regulation of its receptor complex, the structure basis of BRI1 ectodomain and BR recognition, its direct substrates, and the termination of the activated BRI1 receptor complex. [Figure: see text] Xuelu Wang (Corresponding author).

Proteomic analysis of leaves and roots of common wheat (Triticum aestivum L.) under copper-stress conditions

Proteomic studies were performed to identify the protein species involved in copper (Cu) stress responses in common wheat. Two-week-old wheat seedlings were exposed to 100 μM CuSO4 treatment for 3 days. Growth of shoots and roots was markedly inhibited and lipid peroxidation was greatly increased. Cu was readily absorbed by wheat seedlings, with greater Cu contents in roots than in leaves. Using 2-DE method, 98 protein spots showed significantly enhanced or reduced abundance, of which 93 were successfully identified. Of these identified protein species, 49 and 44 were found in roots and leaves, respectively. Abundance of most of identified protein species, which function in signal transduction, stress defense, and energy production, was significantly enhanced, while that of many protein species involved in carbohydrate metabolism, protein metabolism, and photosynthesis was severely reduced. The Cu-responsive protein interaction network revealed 36 key proteins, most of which may be regulated by abscisic acid (ABA), ethylene, jasmonic acid (JA), and so on. Exogenous JA application showed a protective effect against Cu stress and significantly increased transcripts of the glutathione S-transferase (GST) gene. This study provides insight into the molecular mechanisms of Cu responses in higher plants.

An atypical kinase under balancing selection confers broad-spectrum disease resistance in Arabidopsis

The failure of gene-for-gene resistance traits to provide durable and broad-spectrum resistance in an agricultural context has led to the search for genes underlying quantitative resistance in plants. Such genes have been identified in only a few cases, all for fungal or nematode resistance, and encode diverse molecular functions. However, an understanding of the molecular mechanisms of quantitative resistance variation to other enemies and the associated evolutionary forces shaping this variation remain largely unknown. We report the identification, map-based cloning and functional validation of QRX3 (RKS1, Resistance related KinaSe 1), conferring broad-spectrum resistance to Xanthomonas campestris (Xc), a devastating worldwide bacterial vascular pathogen of crucifers. RKS1 encodes an atypical kinase that mediates a quantitative resistance mechanism in plants by restricting bacterial spread from the infection site. Nested Genome-Wide Association mapping revealed a major locus corresponding to an allelic series at RKS1 at the species level. An association between variation in resistance and RKS1 transcription was found using various transgenic lines as well as in natural accessions, suggesting that regulation of RKS1 expression is a major component of quantitative resistance to Xc. The co-existence of long lived RKS1 haplotypes in A. thaliana is shared with a variety of genes involved in pathogen recognition, suggesting common selective pressures. The identification of RKS1 constitutes a starting point for deciphering the mechanisms underlying broad spectrum quantitative disease resistance that is effective against a devastating and vascular crop pathogen. Because putative RKS1 orthologous have been found in other Brassica species, RKS1 provides an exciting opportunity for plant breeders to improve resistance to black rot in crops.

During the evolution of plant-pathogen interactions, plants have evolved the capability to defend themselves from pathogen infection by different overlapping mechanisms. Disease resistance is constituted by an elaborate, multilayered system of defense. Among these responses, quantitative resistance is a prevalent form of resistance in crops and natural plant populations, for which the genetic and molecular bases remain largely unknown. Thus, identification of the genes underlying quantitative resistance constitutes a major challenge in plant breeding and evolutionary biology, and might have enormous practical implications for human health by increasing crop yield and quality. Our work contributes to understanding the molecular bases of quantitative resistance to the vascular pathogen Xanthomonas campestris (Xc), which is responsible for black rot, an important disease of crucifers worldwide. By multiple approaches, we demonstrate that RKS1 is a quantitative resistance gene in Arabidopsis thaliana conferring broad-spectrum resistance to Xc and that this resistance mechanism in plants is associated with regulation of RKS1 expression. We also provide evidence that RKS1 allelic variation is a major component of quantitative resistance to Xc at the species level. Finally, the long-lived polymorphism associated with RKS1 suggests that evolutionary stable broad-spectrum resistance to Xc may be achieved in natural populations of A. thaliana.

Identification and functional analysis of tomato BRI1 and BAK1 receptor kinase phosphorylation sites

Brassinosteroids (BRs) are plant hormones that are perceived at the cell surface by a membrane-bound receptor kinase, BRASSINOSTEROID INSENSITIVE1 (BRI1). BRI1 interacts with BRI1-ASSOCIATED RECEPTOR KINASE1 (BAK1) to initiate a signal transduction pathway in which autophosphorylation and transphosphorylation of BRI1 and BAK1, as well as phosphorylation of multiple downstream substrates, play critical roles. Detailed mechanisms of BR signaling have been examined in Arabidopsis (Arabidopsis thaliana), but the role of BRI1 and BAK1 phosphorylation in crop plants is unknown. As a foundation for understanding the mechanism of BR signaling in tomato (Solanum lycopersicum), we used liquid chromatography-tandem mass spectrometry to identify multiple in vitro phosphorylation sites of the tomato BRI1 and BAK1 cytoplasmic domains. Kinase assays showed that both tomato BRI1 and BAK1 are active in autophosphorylation as well as transphosphorylation of each other and specific peptide substrates with a defined sequence motif. Site-directed mutagenesis revealed that the highly conserved kinase domain activation loop residue threonine-1054 was essential for tomato BRI1 autophosphorylation and peptide substrate phosphorylation in vitro. Furthermore, analysis of transgenic lines expressing full-length tomato BRI1-Flag constructs in the weak tomato bri1 allele, curl3(-abs1), demonstrated that threonine-1054 is also essential for normal BRI1 signaling and tomato growth in planta. Finally, we cloned the tomato ortholog of TGF-β Receptor Interacting Protein (TRIP1), which was previously shown to be a BRI1-interacting protein and kinase domain substrate in Arabidopsis, and found that tomato TRIP1 is a substrate of both tomato BRI1 and BAK1 kinases in vitro.

Autophosphorylation of gatekeeper tyrosine by symbiosis receptor kinase

Plant receptor-like kinases (RLKs) share their evolutionary origin with animal interleukin-1 receptor-associated kinase (IRAK)/Pelle family of soluble kinases and are distinguished by having tyrosine as 'gatekeeper'. This position is adjacent to the hinge region and is hidden in a hydrophobic pocket of the catalytic cleft of protein kinases and is therefore least probable to be a target for any modification. This communication illustrates the accessibility of the gatekeeper site (Y670) towards both autophosphorylation and dephosphorylation in the recombinant cytoplasmic domain of symbiosis receptor kinase from Arachis hypogaea (AhSYMRK). Autophosphorylation on gatekeeper tyrosine was detected prior to extraction but never under in vitro conditions. We hypothesize gatekeeper phosphorylation to be associated with synthesis/maturation of AhSYMRK and this phenomenon may be prevalent among RLKs.

A simple in vitro method to measure autophosphorylation of protein kinases

Receptor-like protein kinases (RLKs) are a large and important group of plant proteins involved in numerous aspects of development and stress response. Within this family, homo-oligermization of receptors followed by autophosphorylation of the intracellular protein kinase domain appears to be a widespread mechanism to regulate protein kinase activity. In vitro studies of several RLKs have identified autophosphorylation sites involved in regulation of catalytic activity and signaling in vivo. Recent work has established that multiple RLKs are biochemically active when expressed in E. coli and readily autophosphorylate prior to purification or subsequent manipulation. This observation has led us to develop a simplified method for assaying RLK phosphorylation status as an indirect measure of intrinsic autophosphorylation activity. The method involves expressing a recombinant RLK protein kinase domain in E. coli, followed by SDS-PAGE of boiled cell lysate, and sequential staining with the phosphoprotein stain Pro-Q Diamond and a colloidal Coomassie total protein stain. We show this method can be used to measure and quantify in vitro autophosphorylation levels of recombinant wildtype and mutant versions of the Arabidopsis RLK HAESA, as well as to detect transphosphorylation activity of recombinant HAESA against a protein kinase inactive version of itself. Our method has several advantages over traditional protein kinase assays. It does not require protein purification, transfer, blotting, or radioactive reagents. It allows for rapid and quantitative assessment of autophosphorylation levels and should have general utility in the study of any autophosphorylating protein kinase expressed in E. coli.

Experimental analysis of receptor kinase phosphorylation

Ligand binding by the extracellular domain of receptor kinases leads to phosphorylation and activation of the cytoplasmic domain of these important membrane-bound signaling proteins. To thoroughly characterize receptor kinase function, it is essential to identify specific phosphorylation sites by mass spectrometry. In this chapter, we summarize an efficient protein purification and modification protocol to prepare receptor kinases for liquid chromatography/tandem mass spectrometry analysis. Both recombinant receptor kinase cytoplasmic domains expressed in bacteria and full-length receptor kinase proteins expressed in living plant tissue are considered, and multiple methods of mass spectrometry are described that allow optimal identification of phosphorylated peptides of both in vitro- and in vivo-derived samples.

Calcium/calmodulin inhibition of the Arabidopsis BRASSINOSTEROID-INSENSITIVE 1 receptor kinase provides a possible link between calcium and brassinosteroid signalling

The receptor kinase BRI1 (BRASSINOSTEROID-INSENSITIVE 1) is a key component in BR (brassinosteroid) perception and signal transduction, and has a broad impact on plant growth and development. In the present study, we demonstrate that Arabidopsis CaM (calmodulin) binds to the recombinant cytoplasmic domain of BRI1 in a Ca2+-dependent manner in vitro. In silico analysis predicted binding to Helix E of the BRI1 kinase subdomain VIa and a synthetic peptide based on this sequence interacted with Ca2+/CaM. Co-expression of CaM with the cytoplasmic domain of BRI1 in Escherichia coli strongly reduced autophosphorylation of BRI1, in particular on tyrosine residues, and also reduced the BRI1-mediated transphosphorylation of E. coli proteins on tyrosine, threonine and presumably serine residues. Several isoforms of CaM and CMLs (CaM-like proteins) were more effective (AtCaM6, AtCaM7 and AtCML8, where At is Arabidopsis thaliana) than others (AtCaM2, AtCaM4 and AtCML11) when co-expressed with BRI1 in E. coli. These results establish a novel assay for recombinant BRI1 transphosphorylation activity and collectively uncover a possible new link between Ca2+ and BR signalling.

Tyrosine Phosphorylation of the BRI1 Receptor Kinase Occurs via a Post-Translational Modification and is Activated by the Juxtamembrane Domain

In metazoans, receptor kinases control many essential processes related to growth and development and response to the environment. The receptor kinases in plants and animals are structurally similar but evolutionarily distinct and thus while most animal receptor kinases are tyrosine kinases the plant receptor kinases are classified as serine/threonine kinases. One of the best studied plant receptor kinases is Brassinosteroid Insensitive 1 (BRI1), which functions in brassinosteroid signaling. Consistent with its classification, BRI1 was shown in early studies to autophosphorylate in vitro exclusively on serine and threonine residues and subsequently numerous specific phosphoserine and phosphothreonine sites were identified. However, several sites of tyrosine autophosphorylation have recently been identified establishing that BRI1 is a dual-specificity kinase. This raises the paradox that BRI1 contains phosphotyrosine but was only observed to autophosphorylate on serine and threonine sites. In the present study, we demonstrate that autophosphorylation on threonine and tyrosine (and presumably serine) residues is a post-translational modification, ruling out a co-translational mechanism that could explain the paradox. Moreover, we show that in general, autophosphorylation of the recombinant protein appears to be hierarchical and proceeds in the order: phosphoserine > phosphothreonine > phosphotyrosine. This may explain why tyrosine autophosphorylation was not observed in some studies. Finally, we also show that the juxtamembrane domain of BRI1 is an activator of the kinase domain, and that kinase specificity (serine/threonine versus tyrosine) can be affected by residues outside of the kinase domain. This may have implications for identification of signature motifs that distinguish serine/threonine kinases from dual-specificity kinases.

Transphosphorylation of E. coli Proteins during Production of Recombinant Protein Kinases Provides a Robust System to Characterize Kinase Specificity

Protein kinase specificity is of fundamental importance to pathway regulation and signal transduction. Here, we report a convenient system to monitor the activity and specificity of recombinant protein kinases expressed in E. coli. We apply this to the study of the cytoplasmic domain of the plant receptor kinase BRASSINOSTEROID-INSENSITIVE 1 (BRI1), which functions in brassinosteroid (BR) signaling. Recombinant BRI1 is catalytically active and both autophosphorylates and transphosphorylates E. coli proteins in situ. Using enrichment approaches followed by LC-MS/MS, phosphosites were identified allowing motifs associated with auto- and transphosphorylation to be characterized. Four lines of evidence suggest that transphosphorylation of E. coli proteins by BRI1 is specific and therefore provides meaningful results: (1) phosphorylation is not correlated with bacterial protein abundance; (2) phosphosite stoichiometry, estimated by spectral counting, is also not related to protein abundance; (3) a transphosphorylation motif emerged with strong preference for basic residues both N- and C-terminal to the phosphosites; and (4) other protein kinases (BAK1, PEPR1, FLS2, and CDPKβ) phosphorylated a distinct set of E. coli proteins and phosphosites. The E. coli transphosphorylation assay can be applied broadly to protein kinases and provides a convenient and powerful system to elucidate kinase specificity.

Deactivation of the Arabidopsis BRASSINOSTEROID INSENSITIVE 1 (BRI1) receptor kinase by autophosphorylation within the glycine-rich loop

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.

Brassinosteroids

Brassinosteroids (BRs) are endogenous plant hormones essential for the proper regulation of multiple physiological processes required for normal plant growth and development. Since their discovery more than 30 years ago, extensive research on the mechanisms of BR action using biochemistry, mutant studies, proteomics and genome-wide transcriptome analyses, has helped refine the BR biosynthetic pathway, identify the basic molecular components required to relay the BR signal from perception to gene regulation, and expand the known physiological responses influenced by BRs. These mechanistic advances have helped answer the intriguing question of how BRs can have such dramatic pleiotropic effects on a broad range of diverse developmental pathways and have further pointed to BR interactions with other plant hormones and environmental cues. This chapter briefly reviews historical aspects of BR research and then summarizes the current state of knowledge on BR biosynthesis, metabolism and signal transduction. Recent studies uncovering novel phosphorelays and gene regulatory networks through which BR influences both vegetative and reproductive development are examined and placed in the context of known BR physiological responses including cell elongation and division, vascular differentiation, flowering, pollen development and photomorphogenesis.