PREPRINTS
Akers JF, Bothe A, Suh H, Jung C, Stolp Z, Ghosh T, Yan L, Wang Y, Grismer TS, Reyes AV, Hu T, Xu SL, Ban N, Kostova KK. (2024) ZNF574 is a Quality Control Factor For Defective Ribosome Biogenesis Intermediates. bioRxiv. DOI: 10.1101/2024.04.26.591394.
Zhang T, Klair A, Tang Z, Reyes AV, Tripka A, Lee J, Gundran K, Noll SE, Wang X, Zare RN, Xu SL, Wang C, Dicksinson AJ. (2024) The metabolite itaconate modulates multiple pathways for plant growth and development. . Submitted.
Reyes AV, Shrestha R, Grimser TS, Byun D, Xu SL. (2024). Impact of alternative splicing on Arabodpsis proteome. bioRxiv. DOI: 10.1101/2024.02.29.582853.
Grismer TS*, Karundasa SS*, Shrestha R, Byun D, Ni W, Reyes AV, Xu SL. (2024) Workflow enhancement of TurboID-mediated proximity labeling for SPY signaling network mapping. bioRxiv. DOI:10.1101/2024.02.17.580820v1.
Powers J, Zhang X, Reyes AV, Zavaliev R, Xu SL, Dong XN. (2024) Next-generation mapping of salicylic acid signaling hub and transcriptional cascade. bioRxiv. DOI:10.1101/2024.01.03.574047
Kim RG, Huang W, Findinier J, Bunbury F, Redekop Petra, Shrestha R, Vilarrasa-Blasi Josep, Jinkerson RE, Fakhimi N, Fauser F, Jonikas MC, Onishi M, Xu SL, Grossman AR. (2023). Chloroplast methyltransferase Homolog RMT2 is involved in photosystem I Biogenesis. bioRxiv. DOI: 10.1101/2023.12.21.572672.
Chaudhary A, Hsiao YC, Yeh FLJ, Wu, HM, Cheung AY, Xu SL, Wang ZY. (2023). Brassinosteroid recruits FERONIA to safeguard cell expansion in Arabidopsis. bioRxiv. DOI: 10.1101/2023.10.01. 560400.
Zhang ZZ, Zhang HL, Gonzalez E, Grismer T, Xu SL, Wang ZY. (2023). UPL3 mediates starvation-induced BZR1 degradation and growth arrest in Arabidopsis. bioRxiv. DOI: 10.1101/2023.10.18.562997.
Shao ZY, Bian LQ, Ahmadi SK, Daniel TJ, Belmonte MA, Burns JG, Kotla P, Bi Y, Shen Z, Xu SL, Wang ZY, Briggs SP, Qiao H. (2023). Nuclear pyruvate dehydrogenase complex regulates histone acetylation and transcription regulation in the ethylene responses in Arabidopsis. bioRxiv. DOI: 10.1101/2023.10.25.564010.
Liu A, Mair A, Matos J, Vollbrecht M, Xu SL, Bergmann D. Cell Fate Programming by Transcription Factors and Epigenetic Machinery in Stomatal Development. (2023) bioRxiv. DOI: 10.1101/2023.08.23.
2024
Wallner E-S, Mair A, Handler D, McWhite CD, Xu SL, Dolan L, Bergmann D. (2024). Spatially resolved proteomics of the Arabidopsis stomatal lineage identifies polarity complexes for cell divisions and stomatal pores. Developmental Cell. 2024. March 21st, doi: 10.1016/j.devcel.2024.03.001.
Yang N, Ren J, Dai S, Wang K, Leung M, Lu Y, An Y, Burlingame A, Xu SL, Wang ZY, Yu W, Li N. (2024). The quantitative biotinylproteomics studies reveal a WInd-Related Kinase 1 (WIRK1) functioning as an early signaling component in wind-induced thigmomorphogenesis and gravitropism. Mol Cell Proteomics. 2024. Feb 15th.doi: 10.1016/j.mcpro.2024.100738.
Shrestha R, Karunadasa S, Grismer T, Reyes AV, Xu SL. (2024) SECRET AGENT O-GlcNAcylates hundreds of proteins involved in diverse cellular processes in Arabidopsis. Mol Cell Proteomics. 2024 Feb 7;:100732. doi: 10.1016/j.mcpro.2024.100732.
2023
Chien YC, Reyes AV, Parka HL, Xu SL, and Yoon GM. (2023) Unveiling the proximal proteome of CTR1 through TurboID-mediated proximity labeling. Proteomics. DOI: 10.1002/pmic.202300212.
Xu SL, Shrestha R, Karunadasa SS, Xie PQ. (2023). Proximity labeling in plants. Annu. Rev. Plant Biol. DOI: 10.1146/annurev-arplant-070522-052132.
Bi Y*, Shrestha R*, Zhang ZZ*, Hsu CC, Reyes AV, Karunadasa S, Baker PR, Maynard JC, Liu Y, Hakimi A, Lopez-Ferrer D, Hassan T, Chalkley RJ, Xu SL#, Wang ZY#. (2023). SPY mediates O-fucose modification of hundreds of proteins and sugar-dependent growth in Arabidopsis. Plant Cell. (Breakthrough Report). (#co-corresponding author). DOI: 10.1093/plcell/koad023.
Kim TW, Park CH, Hsu CC, Kim YW, Ko YW, Zhang Z, Zhu JY, Hsiao Y, Branon T, Kassik K, Saldivar E, Li K, Psha A, Provart NJ, Burlingame AL, Xu SL, Ting AY, Wang ZY. (2023) Mapping the signaling network of BIN2 kinase using TurboID-mediated biotin labeling and phosphoproteomics. Plant Cell. DOI: 10.1093/plcell/koad013.
McKown K, Ximena Anleu M, Mair A, Xu SL, Raissig MT, Bergmann DC. (2023). Extracurricular roles and divergent regulation of FAMA in Brachypodium and Arabidopsis stomatal development. Plant Cell. DOI:10.1093/plcell/koac341.
Davis JA, Reyes, AV, Nitika N, Saha A, Wolfgeher DJ, Xu SL, Truman AW, Li B, Chakrabarti K. (2023). Proteomic analysis defines the interactome of telomerase in the protozoan parasite, Trypanosoma brucei. Front. Cell Dev. Biol. 10.3389/fcell.2023.1110423
2022
Mehta D, Ahkami A, Walley J, Xu SL, Uhrig RG. (2022) Quantitative Proteomics in Plant Science: Time to move beyond the western blot. Nat. Plants. DOI:10.1038/s41477-022-01314-8.
Heazlewood JL, Wallace IS, Xu SL. (2022). Editorial: Advances in plant proteomics. Frontiers in Plant Science. DOI: 10.3389/fpls.2022.1072217
Park CH, Bi Y,Youn JH, Kim JG, Kim SH, Kim JG, Xu NY, Shrestha R, Burlingame AL, Xu SL, Mudgett MB, Kim SK, Kim TW, Wang ZY. (2022) Deconvoluting signals downstream of growth and immune receptor kinases by phosphocodes of the BSU1 family phosphatases. Nat. Plants. DOI: 10.1038/s41477-022-01167-10.
Reyes AV, Shrestha R, Baker PR, Chalkley RJ, Xu SL. (2022). Application of Parallel Reaction Monitoring in 15N labeled Samples for Quantification. Front. Plant Sci., DOI: 10.3389/fpls.2022.832585.
Shrestha R, Reyes AV, Baker PR, Wang ZY, Chalkley RJ, Xu SL. (2022) 15N metabolic labeling quantification workflow in Arabidopsis using Protein Prospector. Front. Plant Sci., DOI: 10.3389/fpls.2022.832562
2017-2021
Bi Y, Deng Z, Ni W, Shrestha R, Savage D, Hartwig T, Patil S, Hong SH, Zhang ZZ, Oses-Prieto JA, Li KH, Quail PH, Burlingame AL, Xu SL#, Wang ZY#. (2021) Arabidopsis ACINUS is O-glycosylated and regulates transcription and alternative splicing of regulators of reproductive transitions. Nat. Commun. DOI: 10.1038/s41467-021-20929-7. (#,co-corresponding author). [highlighted in Faculty Opinions]
Wigington CP, Roy J, Damle NP, Yadav VK, Blikstad C, Resch E, Wong CJ, Mackay DR, Wang JT, Krystkowiak I, Bradburn D, Tsekitsidou E, Hong SH, Kaderali MA, Xu SL, Stearns T, Gingras AC, Ullman KS, Ivarsson Y, Davey NE, Cyert MS. (2020) Systematic discovery of short linear motifs decodes calcineurin phosphatase signaling. Mol Cell. DOI: 10.1016/j.molcel.2020.06.029.
Garcia V, Xu SL, Wang WF, Ravikumar R, Elliott L, Gonzalez E, Fesenko M, Altmann M, Brunschweiger B, Falter-Braun P, Moore I, Buligame AL, Assaad F, Wang ZY. (2020) Proteomic studies of the Arabidopsis TRAPP complexes reveal conserved organization and a novel plant-specific component with a role in plant development. Plant Cell. DOI:10.1105/tpc.20.00044.
Mair A, Xu SL, Branon TC, Ting AY, Bergmann DC. (2019) Proximity labeling of protein complexes and cell-type-specific organellar proteomes in Arabidopsis enabled by TurboID. eLife. DOI: 10.7554/eLife.47864. [highlighted in Faculty Opinions]
Zhao JL, Zhang LQ, Liu N, Xu S, Yue ZL, Zhang LL, Deng Z, Burlingame AL, Sun DY, Wang ZY, Sun Y, Zhang SW. (2019) Mutual regulation of receptor-like kinase SIT1 and B'κ-PP2A shapes the early response of rice to salt stress. Plant Cell. DOI: 10.1105/tpc.18.00706.
Kim EJ, Lee SH, Park CH, Kim SH, Hsu CC, Xu S, Wang ZY, Kim SK, Kim TW. (2019) Plant U-Box40 Mediates Degradation of the Brassinosteroid-Responsive Transcription Factor BZR1 in Arabidopsis Roots. Plant Cell. DOI: 10.1105/tpc.18.00941.
Ni W*, Xu SL*, González-Grandío E, Chalkley RJ, Hühmer AF, Burlingame AL, Wang ZY, and Quail PH. (2017) PPKs mediate direct signal transfer from phytochrome photoreceptors to transcription factor PIF3 in Arabidopsis. Nat. Commun. *equal contribution. DOI: 10.1038/ncomms15236.
Xu SL, Chalkley RJ, Maynard JC, Wang W, Ni W, Jiang XY, Shin K, Cheng L, Savage D, Hühmer AFR, Burlingame AL, Wang ZY. (2017) Proteomic analysis reveals O-GlcNAc modification on proteins with key regulatory functions in Arabidopsis. PNAS., DOI: 10.1073/pnas.1610452114. [highlighted in F1000].
SELECTED PUBLICATION BEFORE 2017
Xu SL, Medzihradszky KF, Wang ZY, Burlingame AL, Chalkley RJ. (2016) N-Glycopeptide Profiling in Arabidopsis Inflorescence. Mol Cell Proteomics. DOI: 10.1074/mcp.M115.056101.
Ni W*, Xu SL*, Tepperman JM, Stanley DJ, Maltby DA, Gross JD, Burlingame AL, Wang ZY and Quail PH. (2014) A mutually assured destruction mechanism attenuates light signaling in Arabidopsis. Science. DOI: 10.1126/science.1250778. [highlighted in F1000]
Ni WM*, Xu SL*, Chalkley RJ, D Pham TN, Guan SH, Maltby DA, Burlingame AL, Wang ZY, Quail PH. (2013). Multisite light-induced phosphorylation of the transcription factor PIF3 is necessary for both its rapid degradation and concomitant negative feedback-modulation of photoreceptor phyB levels in Arabidopsis. Plant Cell. DOI: 10.1105/tpc.113.112342.
Xu SL, Rahman A, Baskin T, Kieber JJ. (2008) Two leucine-rich repeat receptor kinases mediate signaling linking cell wall biosynthesis and ACC synthase in Arabidopsis. Plant Cell. DOI: 10.1105/tpc.108.063354.