دورية أكاديمية
Unveiling orphan receptor-like kinases in plants: novel client discovery using high-confidence library predictions in the Kinase-Client (KiC) assay.
| العنوان: | Unveiling orphan receptor-like kinases in plants: novel client discovery using high-confidence library predictions in the Kinase-Client (KiC) assay. |
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| المؤلفون: | Jorge GL; Division of Biochemistry, C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States., Kim D; Division of Plant Science & Technology, C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States., Xu C; Institute for Data Science and Informatics, C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States., Cho SH; Division of Plant Science & Technology, C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States., Su L; Department of Electrical Engineering and Computer Science, C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States.; Shandong University of Science and Technology, Qingdao, Shandong, China., Xu D; Department of Electrical Engineering and Computer Science, C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States., Bartley LE; Institute of Biological Chemistry, Washington State University, Pullman, WA, United States., Stacey G; Division of Plant Science & Technology, C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States., Thelen JJ; Division of Biochemistry, C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States. |
| المصدر: | Frontiers in plant science [Front Plant Sci] 2024 Apr 03; Vol. 15, pp. 1372361. Date of Electronic Publication: 2024 Apr 03 (Print Publication: 2024). |
| نوع المنشور: | Journal Article |
| اللغة: | English |
| بيانات الدورية: | Publisher: Frontiers Research Foundation Country of Publication: Switzerland NLM ID: 101568200 Publication Model: eCollection Cited Medium: Print ISSN: 1664-462X (Print) Linking ISSN: 1664462X NLM ISO Abbreviation: Front Plant Sci Subsets: PubMed not MEDLINE |
| أسماء مطبوعة: | Original Publication: Lausanne : Frontiers Research Foundation, 2010- |
| مستخلص: | Plants are remarkable in their ability to adapt to changing environments, with receptor-like kinases (RLKs) playing a pivotal role in perceiving and transmitting environmental cues into cellular responses. Despite extensive research on RLKs from the plant kingdom, the function and activity of many kinases, i.e., their substrates or "clients", remain uncharted. To validate a novel client prediction workflow and learn more about an important RLK, this study focuses on P2K1 (DORN1), which acts as a receptor for extracellular ATP (eATP), playing a crucial role in plant stress resistance and immunity. We designed a Kinase-Client (KiC) assay library of 225 synthetic peptides, incorporating previously identified P2K phosphorylated peptides and novel predictions from a deep-learning phosphorylation site prediction model (MUsite) and a trained hidden Markov model (HMM) based tool, HMMER. Screening the library against purified P2K1 cytosolic domain (CD), we identified 46 putative substrates, including 34 novel clients, 27 of which may be novel peptides, not previously identified experimentally. Gene Ontology (GO) analysis among phosphopeptide candidates revealed proteins associated with important biological processes in metabolism, structure development, and response to stress, as well as molecular functions of kinase activity, catalytic activity, and transferase activity. We offer selection criteria for efficient further in vivo experiments to confirm these discoveries. This approach not only expands our knowledge of P2K1's substrates and functions but also highlights effective prediction algorithms for identifying additional potential substrates. Overall, the results support use of the KiC assay as a valuable tool in unraveling the complexities of plant phosphorylation and provide a foundation for predicting the phosphorylation landscape of plant species based on peptide library results. Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The author(s) declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision. (Copyright © 2024 Jorge, Kim, Xu, Cho, Su, Xu, Bartley, Stacey and Thelen.) |
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| معلومات مُعتمدة: | R01 GM121445 United States GM NIGMS NIH HHS |
| فهرسة مساهمة: | Keywords: P2K1; deep learning; extracellular ATP; in vitro screening; phosphopeptides; protein kinase |
| تواريخ الأحداث: | Date Created: 20240418 Latest Revision: 20240426 |
| رمز التحديث: | 20240426 |
| مُعرف محوري في PubMed: | PMC11021772 |
| DOI: | 10.3389/fpls.2024.1372361 |
| PMID: | 38633461 |
| قاعدة البيانات: | MEDLINE |
Full Text Finder | تدمد: | 1664-462X |
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| DOI: | 10.3389/fpls.2024.1372361 |