Deconvoluting signals downstream of growth and immune receptor kinases by phosphocodes of the BSU1 family phosphatases

Park, Chan Ho; Bi, Yang; Youn, Ji-Hyun; Kim, So-Hee; Kim, Jung‐Gun; Xu, Nicole Y; Shrestha, Ruben; Burlingame, Alma L.; Xu, Shou-Ling; Mudgett, Mary Beth; Kim, Seong‐Ki; Kim, Tae‐Wuk; Wang, Wenfei

doi:10.1038/s41477-022-01167-1

Cited by 14 publications

(8 citation statements)

References 44 publications

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“…Recent study reveals that loss of BSU1 family phosphatases activates effector-triggered immunity (ETI) and impairs flagellin-triggered MAP kinase activation and immunity, the mechanism of which is that BIK1 enhances the flagellin-induced MAP kinase activation and immunity through phosphorylating BSU1 at serine-251 (S251), whereas it does not affect immune signaling by phosphorylating at S764, an important phosphorylation site mediating the interaction between BSU1 and BIN2, of which BIN2 is induced by CDG1 in BRs-BRI1 signaling. These results indicate that BSU1 plays an essential role in immunity and transduces BR-BRI1 and flagellin-FLS2 signals by different phosphorylation sites …”

Section: Crosstalk Between Brs Signal and Immune Signalsmentioning

confidence: 81%

“…These results indicate that BSU1 plays an essential role in immunity and transduces BR-BRI1 and flagellin-FLS2 signals by different phosphorylation sites. 99 43 At the signal transduction level, the crosstalk between the BR signal and the PTI signal is mainly based on BIK1/BSK1/BSU1/BIN2. BIK1 mediates inverse functions in the PTI and BR signals via dynamic association with specific receptor complexes and differential phosphorylation events.…”

Section: Functions Of Brs In Pathogen Resistancementioning

confidence: 99%

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Roles of Brossinosteroids Signaling in Biotic and Abiotic Stresses

TingShan

Xie

Zhou

et al. 2023

J. Agric. Food Chem.

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Brassinosteroids (BRs) are a group of plant-specific steroidal phytohormones, which play fundamental roles in regulating diverse aspects of the plant life cycle including plant growth, development, and stress response. Extensive studies have demonstrated that BRs signaling is involved in plant innate immunity as well as the response to environmental stimuli including extreme temperatures, saline-alkali, and drought. In addition, that the BRs signal interacts with other immune-related signals, constructing a complex signal network to regulate plant−microbe interactions and adaptation to adverse environments, has also been preliminarily explored. A timely and updated review on these progresses is of great significance for understanding BRs functions, improving the BRs regulation network and breeding disease-resistant crops, meantime with higher tolerance to abiotic stresses. Here, we mainly focus on the latest advances in the BRs signal which regulate plant defense and tolerance to abiotic and biotic stresses and then further highlight the crosstalk between the BRs signal and other immune-related or stress response pathways, with an aim to use them to improve crops by transgenic technologies.

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Section: Crosstalk Between Brs Signal and Immune Signalsmentioning

confidence: 81%

Section: Functions Of Brs In Pathogen Resistancementioning

confidence: 99%

Roles of Brossinosteroids Signaling in Biotic and Abiotic Stresses

TingShan

Xie

Zhou

et al. 2023

J. Agric. Food Chem.

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“…For a concise prediction comparison, we compiled a short list of functionally important phosphosites, validated in A. thaliana , involved in the brassinosteroid (BR), ethylene (ET), and abscisic acid (ABA) pathways. In the BR pathway, we included BRASSINOSTEROID INSENSITIVE 1 (BRI1) Y831 and Y956 (Bojar et al, 2014 ; Oh et al, 2009 ), BRASSINOSTEROID‐INSENSITIVE2 (BIN2) S187, S203, and Y200 (Kim et al, 2009 ; Xiong et al, 2017 ), BRASSINAZOLE RESISTANT1 (BZR1) Thr173 and Thr177 (Ryu et al, 2007 ), and BRI1‐SUPPRESSOR1 (BSU1) Ser251 and Ser764 (Park et al, 2022 ). In the ET pathway, we included ETHYLENE INSENSITIVE3 (EIN3) Thr174 and Thr592 (Zhao & Guo, 2011 ) and ACC SYNTHASE 6 Ser480, Ser483, and Ser488 (Liu & Zhang, 2004 ).…”

Section: Resultsmentioning

confidence: 99%

PhosBoost: Improved phosphorylation prediction recall using gradient boosting and protein language models

Poretsky,

Andorf,

Sen

2023

Plant Direct

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Protein phosphorylation is a dynamic and reversible post‐translational modification that regulates a variety of essential biological processes. The regulatory role of phosphorylation in cellular signaling pathways, protein–protein interactions, and enzymatic activities has motivated extensive research efforts to understand its functional implications. Experimental protein phosphorylation data in plants remains limited to a few species, necessitating a scalable and accurate prediction method. Here, we present PhosBoost, a machine‐learning approach that leverages protein language models and gradient‐boosting trees to predict protein phosphorylation from experimentally derived data. Trained on data obtained from a comprehensive plant phosphorylation database, qPTMplants, we compared the performance of PhosBoost to existing protein phosphorylation prediction methods, PhosphoLingo and DeepPhos. For serine and threonine prediction, PhosBoost achieved higher recall than PhosphoLingo and DeepPhos (.78, .56, and .14, respectively) while maintaining a competitive area under the precision‐recall curve (.54, .56, and .42, respectively). PhosphoLingo and DeepPhos failed to predict any tyrosine phosphorylation sites, while PhosBoost achieved a recall score of .6. Despite the precision‐recall tradeoff, PhosBoost offers improved performance when recall is prioritized while consistently providing more confident probability scores. A sequence‐based pairwise alignment step improved prediction results for all classifiers by effectively increasing the number of inferred positive phosphosites. We provide evidence to show that PhosBoost models are transferable across species and scalable for genome‐wide protein phosphorylation predictions. PhosBoost is freely and publicly available on GitHub.

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“…Protein phosphocodes refer to a set of phosphorylated residues of a protein that is “encoded” by a specific kinase(s) and/or “decoded” by specific signaling molecules ( 37 – 40 ). Both MAPKs and BIN2, a kinase that mediate brassinosteroid signaling and stomatal asymmetric cell division, suppress SPCH proteins, and they appear to “write” a similar code on SPCH, at least within its MPKTD region ( 22 , 26 , 41 ).…”

Section: Discussionmentioning

confidence: 99%

Abscisic acid regulates stomatal production by imprinting a SnRK2 kinase–mediated phosphocode on the master regulator SPEECHLESS

Yang

Zhou

et al. 2022

Sci. Adv.

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Stomata, the epidermal pores for gas exchange between plants and the atmosphere, are the major sites of water loss. During water shortage, plants limit the formation of new stoma via the phytohormone abscisic acid (ABA) to conserve water. However, how ABA suppresses stomatal production is largely unknown. Here, we demonstrate that three core SnRK2 kinases of ABA signaling inhibit the initiation and proliferation of the stomatal precursors in Arabidopsis . We show that the SnRK2s function within the precursors and directly phosphorylate SPEECHLESS (SPCH), the master transcription factor for stomatal initiation. We identify specific SPCH residues targeted by the SnRK2s, which mediate the ABA/drought-induced suppression of SPCH and stomatal production. This SnRK2-specific SPCH phosphocode connects stomatal development with ABA/drought signals and enables the independent control of this key water conservation response. Our work also highlights how distinct signaling activities can be specifically encoded on a master regulator to modulate developmental plasticity.

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Deconvoluting signals downstream of growth and immune receptor kinases by phosphocodes of the BSU1 family phosphatases

Cited by 14 publications

References 44 publications

Roles of Brossinosteroids Signaling in Biotic and Abiotic Stresses

Roles of Brossinosteroids Signaling in Biotic and Abiotic Stresses

PhosBoost: Improved phosphorylation prediction recall using gradient boosting and protein language models

Abscisic acid regulates stomatal production by imprinting a SnRK2 kinase–mediated phosphocode on the master regulator SPEECHLESS

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