Quantitative phosphoproteomic analyses provide evidence for extensive phosphorylation of regulatory proteins in the rhizobia–legume symbiosis

Zhang, Zaibao; Ke, Danxia; Hu, Menghui; Zhang, Chi; Deng, Lijun; Li, Yuting; Li, Jiuli; Zhao, Hongbo; Cheng, Lin; Wang, Lei; Yuan, Hongyu

doi:10.1007/s11103-019-00857-3

Cited by 8 publications

(5 citation statements)

References 89 publications

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“…In contrast to the extensive knowledge on the pre‐mRNA processing factors regulated by phosphorylation in metazoa, very little is known about this topic in plants. Phosphoproteomics data reveal extensive in vivo phosphorylation of RNA metabolism‐related proteins in plants (Wang et al ., 2013; Zhang et al ., 2019; Li et al ., 2022; Domingo et al ., 2023). Till now, several protein kinases from three families (SRPK, AFC and PRP4K) have been reported to regulate splicing factor functions in plant biology (Gallo et al ., 2022; Jin, 2022).…”

Section: Discussionmentioning

confidence: 99%

Regulation of plant resistance to salt stress by the SnRK1‐dependent splicing factor SRRM1L

Sun,

Liu

et al. 2024

New Phytologist

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Summary Most splicing factors are extensively phosphorylated but their physiological functions in plant salt resistance are still elusive. We found that phosphorylation by SnRK1 kinase is essential for SRRM1L nuclear speckle formation and its splicing factor activity in plant cells. In Arabidopsis, loss‐of‐function of SRRM1L leads to the occurrence of alternative pre‐mRNA splicing events and compromises plant resistance to salt stress. In Arabidopsis srrm1l mutant line, we identified an intron‐retention Nuclear factor Y subunit A 10 (NFYA10) mRNA variant by RNA‐Seq and found phosphorylation‐dependent RNA‐binding of SRRM1L is indispensable for its alternative splicing activity. In the wild‐type Arabidopsis, salt stress can activate SnRK1 to phosphorylate SRRM1L, triggering enrichment of functional NFYA10.1 variant to enhance plant salt resistance. By contrast, the Arabidopsis srrm1l mutant accumulates nonfunctional NFYA10.3 variant, sensitizing plants to salt stress. In summary, this work deciphered the molecular mechanisms and physiological functions of SnRK1‐SRRM1L‐NFYA10 module, shedding light on a regulatory pathway to fine‐tune plant adaptation to abiotic stress at the post‐transcriptional and post‐translational levels.

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Section: Discussionmentioning

confidence: 99%

Regulation of plant resistance to salt stress by the SnRK1‐dependent splicing factor SRRM1L

Sun,

Liu

et al. 2024

New Phytologist

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“…Protein phosphorylation is a universal PTM; however, the abundance of phosphorylation largely varies among different species. In C. moschata, the abundance of phosphorylated protein (2,853 phosphorylated proteins) was higher than most of the published species, such as Sus domesticus (966 phosphorylated proteins), Bombyx mori (2,112 phosphorylated proteins), Kandelia candel (1,516 phosphorylated proteins), Nicotiana tabacum (1,311 phosphorylated proteins), Lotus japonicus (1,154 phosphorylated proteins), Ammopiptanthus mongolicus (2,019 phosphorylated proteins), Catalpa fargesii (1,646 phosphorylated proteins), Abelmoschus esculentus (2,550 phosphorylated proteins), and Physcomitrella patens (1,873 phosphorylated proteins) 35,43,45,[50][51][52][53] . High-throughput method gives us an opportunity to screen potential phosphorylated proteins and reveal the involvement of protein phosphorylation in the responses to the C/NDRV infections.…”

Section: Discussionmentioning

confidence: 99%

The phosphoproteomic responses of duck (Cairna moschata) to classical/novel duck reovirus infections in the spleen tissue

Yun

Hua

et al. 2020

Sci Rep

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Duck reovirus (DRV) is a fatal member of the genus Orthoreovirus in the family Reoviridae. The disease caused by DRV leads to huge economic losses to the duck industry. Post-translational modification is an efficient strategy to enhance the immune responses to virus infection. However, the roles of protein phosphorylation in the responses of ducklings to Classic/Novel DRV (C/NDRV) infections are largely unknown. Using a high-resolution LC–MS/MS integrated to highly sensitive immune-affinity antibody method, phosphoproteomes of Cairna moschata spleen tissues under the C/NDRV infections were analyzed, producing a total of 8,504 phosphorylation sites on 2,853 proteins. After normalization with proteomic data, 392 sites on 288 proteins and 484 sites on 342 proteins were significantly changed under the C/NDRV infections, respectively. To characterize the differentially phosphorylated proteins (DPPs), a systematic bioinformatics analyses including Gene Ontology annotation, domain annotation, subcellular localization, and Kyoto Encyclopedia of Genes and Genomes pathway annotation were performed. Two important serine protease system-related proteins, coagulation factor X and fibrinogen α-chain, were identified as phosphorylated proteins, suggesting an involvement of blood coagulation under the C/NDRV infections. Furthermore, 16 proteins involving the intracellular signaling pathways of pattern-recognition receptors were identified as phosphorylated proteins. Changes in the phosphorylation levels of MyD88, NF-κB, RIP1, MDA5 and IRF7 suggested a crucial role of protein phosphorylation in host immune responses of C. moschata. Our study provides new insights into the responses of ducklings to the C/NDRV infections at PTM level.

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“…The dynamic phosphorylation and dephosphorylation of SR proteins plays a role in their subcellular distribution and protein–protein interactions, and in their post-splicing activities in mRNA export, stability, and translation. During rhizobia colonization and infection of Lotus japonicas , most SR proteins were found to be multiply phosphorylated [ 64 ]. The SRPK4 (SR protein-specific kinase 4) and MAPKs (mitogen-activated PKs) were found to phosphorylate SCL30, but SCL30 was targeted by different PKs [ 3 ].…”

Section: The Regulation Of Sr Proteinsmentioning

confidence: 99%

“…The transcription activity of the cell and protein (de)phosphorylation regulates the intranuclear distribution of SR 45 [ 65 ]. The RNA splicing and brassinosteroid (BR) signaling pathways were extensively affected by phosphorylation, and most SR proteins were multiply phosphorylated [ 64 ].…”

Section: The Regulation Of Sr Proteinsmentioning

confidence: 99%

“…Several SR proteins could affect growth as critical regulators of Zn, Mn, and P nutrition, and P uptake and remobilization between leaves and shoots in rice [ 80 ]. As mentioned above, the SR proteins interacted with kinases [ 3 ] and were regulated by phosphorylation and dephosphorylation [ 64 ]. Thus, the specific phosphorylation mechanism is involved in the SR protein, then differentially regulates the function of a plant splicing activator in physiologically and morphologically distinct plant tissues.…”

Section: Sr Proteins Function In the Growth And Stress Responsementioning

confidence: 99%

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Regulatory Network of Serine/Arginine-Rich (SR) Proteins: The Molecular Mechanism and Physiological Function in Plants

Jin

2022

IJMS

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Serine/arginine-rich (SR) proteins are a type of splicing factor. They play significant roles in constitutive and alternative pre-mRNA splicing, and are involved in post-splicing activities, such as mRNA nuclear export, nonsense-mediated mRNA decay, mRNA translation, and miRNA biogenesis. In plants, SR proteins function under a complex regulatory network by protein–protein and RNA–protein interactions between SR proteins, other splicing factors, other proteins, or even RNAs. The regulatory networks of SR proteins are complex—they are regulated by the SR proteins themselves, they are phosphorylated and dephosphorylated through interactions with kinase, and they participate in signal transduction pathways, whereby signaling cascades can link the splicing machinery to the exterior environment. In a complex network, SR proteins are involved in plant growth and development, signal transduction, responses to abiotic and biotic stresses, and metabolism. Here, I review the current status of research on plant SR proteins, construct a model of SR proteins function, and ask many questions about SR proteins in plants.

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Quantitative phosphoproteomic analyses provide evidence for extensive phosphorylation of regulatory proteins in the rhizobia–legume symbiosis

Cited by 8 publications

References 89 publications

Regulation of plant resistance to salt stress by the SnRK1‐dependent splicing factor SRRM1L

Regulation of plant resistance to salt stress by the SnRK1‐dependent splicing factor SRRM1L

The phosphoproteomic responses of duck (Cairna moschata) to classical/novel duck reovirus infections in the spleen tissue

Regulatory Network of Serine/Arginine-Rich (SR) Proteins: The Molecular Mechanism and Physiological Function in Plants

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