Xu Lab

Xu group is currently focusing on :1) method development on XL-MS for structrual analysis of complex protein assembly, such as splicing complex and photosynthesis apparatus; 2) improvement on enrichment and detection of sugar-modified and lysine-methylated proteins in plants; 3) functional studies of the PTM,esp. O-GlcNAcylation, on proteins in plants. 4) Cell altas using crosslinking mass spectrometry and proximity labeling mass spectrometry.

Funding resources: NIH R01, Carnegie Endowment and Venture grant.

Lab Tabs

News

Feb

2021

A plant’s nutrient-sensing abilities can modulate its response to environmental stress

By Carnegie HQ

Palo Alto, CA— Understanding how plants respond to stressful environmental conditions is crucial to developing effective strategies for protecting important agricultural crops from a changing climate. New research led by Carnegie’s Zhiyong Wang, ...

Lab PI

Shouling Xu

Research Scientist

Plant Biology

Carnegie Institution for Science

sxu@carnegiescience.edu
650-739-4225
Office:
260 Panama Street
Stanford, CA 94305, US

Profile

Affiliation

Affiliation:

DPB Faculty

DPB Employees

Labs:

Xu Lab

2017-present: Director of Proteomics Facility, Carnegie Institution at Stanford

2017-present: Principal Investigator/Research Scientist, Carnegie Institution at Stanford

2008, Ph.D, University of North Carolina at Chapel Hill

Teaching

Websites

Facility website

Carnegie Mass Spectrometry Facility

Stanford Links

Xu lab

Lab Members

Sergio Agramont-Justiniano (Research Assistant)
Danbi Byun (Research Associate)
I graduated from UC Davis with B.S. degree in Biotechnology with Outstanding Undergraduate Accomplishment Award from the Plant Sciences Department. I joined the Xu lab in January 2019. My research direction is adapting proteomic tools to study molecular machineries and cell atlas in plants. Before I joined Carnegie, I interned at a neurophysiology lab in UC Davis and worked at several dental offices as a predental student. In my freetime, I enjoy making pottery, traveling, and watching animal videos.
Ajeet Chaudhary (Postdoctoral Fellow)
Megan Chin (Research Assistant)
Sumudu Karunadasa (Postdoctoral Fellow)
I received my B.Sc. degree in Molecular Biology and Biotechnology from University of Peradeniya, Kandy, Sri Lanka. I graduated from University of Kentucky, USA in Plant Molecular Biology. I am interested in discovering plant molecular mechanisms.
Andres Reyes (Research Assistant)
I am an early career researcher with a strong background in molecular biology and bioinformatics. I am passionate about combining my unique skill set of software engineering and proteomics in making meaningful contributions to science while tackling a variety of important biological questions. Currently I contribute to the Xu Lab and the Mass Spectrometry Facility at the Carnegie Institute of Science, Stanford. My research focus in the Xu Lab is exploring selective O-Fucose/O-GlucNAc modifications to dissect biological functions of target proteins, specifically alternative splicing protein complexes. In the Mass Spectrometry Facility, I manage the mass spectrometer and help develop methods in quantitative proteomics from the sample processing to the downstream bioinformatics.
Ruben Shrestha (Postdoctoral Fellow)

Alumni:

Malika Kaderali, Research Assistant, now at Temple University medical school

Su Hyun Hong, Research Associate

Kevin Li, high school Summer Intern, now in UC Santa Barara

Clement Bouden, Summer Intern. Stanford University

Matthew Webb, Summer Intern

Iris Wang, RA

Publications

Reyes AV, Shrestha R, Baker PR, Chalkley RJ, Xu SL. Application of Parallel Reaction Monitoring in 15N labeled Samples for Quantification. 2021. BioRxiv. https://doi.org/10.1101/2021.12.01.470846

Park CH, Bi Y, Youn JH, Kim JG, Shrestha R, Xu N, Xu SL, Mudgett SK, Kim TW, Wang ZY. BSUI family phosphatases mediate Flagellin-FLS2 signaling through a specific phosphocode. 2022. Nature Plant. Accepted. doi: https://doi.org/10.1101/685610.

Shrestha R, Reyes AV, Baker PR, Wang ZY, Chalkley RJ, Xu SL. 15N metabolic labeling quantification workflow in Arabidopsis using Protein Prospector. 2022. Front. Plant Sci., doi.org/10.3389/fpls.2022.832562

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‡. Arabidopsis ACINUS is O-glycosylated and regulates transcription and alternative splicing of regulators of reproductive transitions. 2021. Nat Commun. (‡corresponding authors). https://doi.org/10.1038/s41467-021-20929-7

CP Wigington, J Roy, Damle NP, VK Yadav, C Blikstad, E Resch, CJ Wong, DR Mackay, JT Wang, I Krystkowiak, DA Bradburn, E Tsekitsidou, HY Su, MA Kaderali, S-L Xu, T Stearns, A-C Gingras, KS Ullman, Y Ivarsson, NE Davey, Cyert, MS.Systematic discovery of Short Linear Motifs decodes calcineurin phosphatase signaling. 2020. Mol Cell. https://doi.org/10.1016/j.molcel.2020.06.029

Garcia VJ, Xu SL, Raksha R, Wang W, Elliott L, Fensenko M, Altmann M, Falter-Braun, P, Moore I, Assadd FF, Wang ZY. Proteomic Studies of the Arabidopsis TRAPP complexes reveal conserved organization and a novel plant-specific component with a role in plant development. 2020. Plant Cell. DOI:https://doi.org/10.1105/tpc.20.00044.

Zhao JL, Zhang N, Liu LQ, Xu SL, Yue ZL, Zhang LL, Deng Z, Burlingame AL, Su DY, Wang ZY, Sun Y, Zhang SW. Mutual Regulation of receptor-like kinase SIT and B'k-PP2A shapes the early response of rice to salt stress. 2019. Plant Cell. DOI: https://doi.org/10.1105/tpc.18.00706

Kim TW, Park CH, Hsu CC, Zhu JY, Hsiao Y, Branon TC, Xu SL, Ting AY, Wang ZY. Application of TurboID-mediated proximity labeling for mapping a GSK3 kinase signaling network in Arabidopsis. 2019. BioRxiv . doi: https://doi.org/10.1101/636324

Mair A, Xu SL, Branon TC, Ting AY, Bergmann DC. Proximity labeling of protein complexes and cell-type specific organellar proteomes in Arabidopsis enabled by TurboID. 2019. eLIFE. DOI: 10.7554/eLife.47864

Kim EJ, Lee SH, Park CH, Kim SH, Hsu CC, Xu S, Wang Z, Kim SK, Kim TW. Plant U-Box 40 Mediates Degradation of the Brassinosteroid-Responsive Transcription Factor BZR1 in Arabidopsis Roots. PLANT CELL. 2019. DOI: https://doi.org/10.1105/tpc.18.00941

Xu SL, Chalkley JR, Maynard JC, Wang W, Ni W, Jiang XY, Shin K, Cheng L, Savage D, Huhmer AFR, Burlingame AL, and Wang ZY. 2017. Proteomic analysis reveals O-GlcNAc modification on proteins with key regulatory functions in Arabidopsis. PNAS, 114, E1536–E1543. [ PubMed]

Ni W*, Xu SL*, Grandio EG, Chalkley RJ, Huhmer AF, Burlingame AL , Wang ZY and Quail PH . 2017. PPKs mediate direct signal transfer from phytochrome photoreceptors to transcription factor PIF3. Nat Commun , 8, 15236. [PubMed] Highlighted in F1000.

Xu SL, Medzihradszky KF, Wang ZY, Burlingame AL, Chalkley RJ. 2016.N-Glycopeptide profiling in Arabidopsis inflorescence.MCP. 15(6), 2048-2054. [ PubMed].

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 , 344, 1160-64. [ PubMed] Highlighted by Hines (2014), Highlighted in F1000; Spotlighted by Zhu & Huq, 2014.

Kim EJ, Youn JH, Park CH, Kim TW, Guan S, Xu S, Burlingame AL, Kim YP, Kim SK, Wang ZY, Kim TW. 2016. Oligomerization between BSU1 Family Members Potentiates Brassinosteroid Signaling in Arabidopsis. Mol Plant , 9(1): 178-181. [ PubMed]

Xu P*, Xu SL*, Li ZJ, Tang W, Burlingame AL, Wang ZY. 2014. A brassinosteroid-signaling kinase interacts with multiple receptor-like kinases in Arabidopsis.Mol Plant , 7(2):441-4. [ PubMed]

Ni W *, Xu SL *, Chalkley RJ , Pham TN , Guan S , Maltby DA , Burlingame AL , Wang ZY and 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, 25: 2679-98. [ PubMed]