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Zemaitis KJ, Lin VS, Ahkami AH, Winkler TE, Anderton CR, Veličković D. Expanded Coverage of Phytocompounds by Mass Spectrometry Imaging Using On-Tissue Chemical Derivatization by 4-APEBA. Anal Chem 2023; 95:12701-12709. [PMID: 37594382 DOI: 10.1021/acs.analchem.3c01345] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/19/2023]
Abstract
Probing the entirety of any species metabolome is an analytical grand challenge, especially on a cellular scale. Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) is a common spatial metabolomics assay, but this technique has limited molecular coverage for several reasons. To expand the application space of spatial metabolomics, we developed an on-tissue chemical derivatization (OTCD) workflow using 4-APEBA for the confident identification of several dozen elusive phytocompounds. Overall, this new OTCD method enabled the annotation of roughly 280 metabolites, with only a 10% overlap in metabolic coverage when compared to analog negative ion mode MALDI-MSI on serial sections. We demonstrate that 4-APEBA outperforms other derivatization agents by providing: (1) broad specificity toward carbonyls, (2) low background, and (3) introduction of bromine isotopes. Notably, the latter two attributes also facilitate more confidence in our bioinformatics for data processing. The workflow detailed here trailblazes a path toward spatial hormonomics within plant samples, enhancing the detection of carboxylates, aldehydes, and plausibly other carbonyls. As such, several phytohormones, which have various roles within stress responses and cellular communication, can now be spatially profiled, as demonstrated in poplar root and soybean root nodule.
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Affiliation(s)
- Kevin J Zemaitis
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Vivian S Lin
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Amir H Ahkami
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Tanya E Winkler
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Christopher R Anderton
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Dušan Veličković
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
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Zhou M, Abdali SH, Dilworth D, Liu L, Cole B, Malhan N, Ahkami AH, Winkler TE, Hollingsworth J, Sievert J, Dahlberg J, Hutmacher R, Madera M, Owiti JA, Hixson KK, Lemaux PG, Jansson C, Paša-Tolić L. Isolation of Histone from Sorghum Leaf Tissue for Top Down Mass Spectrometry Profiling of Potential Epigenetic Markers. J Vis Exp 2021. [PMID: 33749685 DOI: 10.3791/61707] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Histones belong to a family of highly conserved proteins in eukaryotes. They pack DNA into nucleosomes as functional units of chromatin. Post-translational modifications (PTMs) of histones, which are highly dynamic and can be added or removed by enzymes, play critical roles in regulating gene expression. In plants, epigenetic factors, including histone PTMs, are related to their adaptive responses to the environment. Understanding the molecular mechanisms of epigenetic control can bring unprecedented opportunities for innovative bioengineering solutions. Herein, we describe a protocol to isolate the nuclei and purify histones from sorghum leaf tissue. The extracted histones can be analyzed in their intact forms by top-down mass spectrometry (MS) coupled with online reversed-phase (RP) liquid chromatography (LC). Combinations and stoichiometry of multiple PTMs on the same histone proteoform can be readily identified. In addition, histone tail clipping can be detected using the top-down LC-MS workflow, thus, yielding the global PTM profile of core histones (H4, H2A, H2B, H3). We have applied this protocol previously to profile histone PTMs from sorghum leaf tissue collected from a large-scale field study, aimed at identifying epigenetic markers of drought resistance. The protocol could potentially be adapted and optimized for chromatin immunoprecipitation-sequencing (ChIP-seq), or for studying histone PTMs in similar plants.
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Affiliation(s)
- Mowei Zhou
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory
| | - Shadan H Abdali
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory
| | - David Dilworth
- DOE-Joint Genome Institute, Lawrence Berkeley Laboratory
| | - Lifeng Liu
- DOE-Joint Genome Institute, Lawrence Berkeley Laboratory
| | - Benjamin Cole
- DOE-Joint Genome Institute, Lawrence Berkeley Laboratory
| | - Neha Malhan
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory
| | - Amir H Ahkami
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory
| | - Tanya E Winkler
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory
| | - Joy Hollingsworth
- Kearney Agricultural Research and Extension Center, University of California Agriculture and Natural Resources
| | - Julie Sievert
- Kearney Agricultural Research and Extension Center, University of California Agriculture and Natural Resources
| | - Jeff Dahlberg
- Kearney Agricultural Research and Extension Center, University of California Agriculture and Natural Resources
| | - Robert Hutmacher
- West Side Research and Extension Center, University of California; Department of Plant Sciences, University of California, Davis
| | - Mary Madera
- Department of Plant and Microbial Biology, University of California, Berkeley
| | - Judith A Owiti
- Department of Plant and Microbial Biology, University of California, Berkeley
| | - Kim K Hixson
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory
| | - Peggy G Lemaux
- Department of Plant and Microbial Biology, University of California, Berkeley
| | - Christer Jansson
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory;
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Varga T, Hixson KK, Ahkami AH, Sher AW, Barnes ME, Chu RK, Battu AK, Nicora CD, Winkler TE, Reno LR, Fakra SC, Antipova O, Parkinson DY, Hall JR, Doty SL. Endophyte-Promoted Phosphorus Solubilization in Populus. Front Plant Sci 2020; 11:567918. [PMID: 33193494 PMCID: PMC7609660 DOI: 10.3389/fpls.2020.567918] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 09/25/2020] [Indexed: 05/24/2023]
Abstract
Phosphorus is one of the essential nutrients for plant growth, but it may be relatively unavailable to plants because of its chemistry. In soil, the majority of phosphorus is present in the form of a phosphate, usually as metal complexes making it bound to minerals or organic matter. Therefore, inorganic phosphate solubilization is an important process of plant growth promotion by plant associated bacteria and fungi. Non-nodulating plant species have been shown to thrive in low-nutrient environments, in some instances by relying on plant associated microorganisms called endophytes. These microorganisms live within the plant and help supply nutrients for the plant. Despite their potential enormous environmental importance, there are a limited number of studies looking at the direct molecular impact of phosphate solubilizing endophytic bacteria on the host plant. In this work, we studied the impact of two endophyte strains of wild poplar (Populus trichocarpa) that solubilize phosphate. Using a combination of x-ray imaging, spectroscopy methods, and proteomics, we report direct evidence of endophyte-promoted phosphorus uptake in poplar. We found that the solubilized phosphate may react and become insoluble once inside plant tissue, suggesting that endophytes may aid in the re-release of phosphate. Using synchrotron x-ray fluorescence spectromicroscopy, we visualized the nutrient phosphorus inside poplar roots inoculated by the selected endophytes and found the phosphorus in both forms of organic and inorganic phosphates inside the root. Tomography-based root imaging revealed a markedly different root biomass and root architecture for poplar samples inoculated with the phosphate solubilizing bacteria strains. Proteomics characterization on poplar roots coupled with protein network analysis revealed novel proteins and metabolic pathways with possible involvement in endophyte enriched phosphorus uptake. These findings suggest an important role of endophytes for phosphorus acquisition and provide a deeper understanding of the critical symbiotic associations between poplar and the endophytic bacteria.
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Affiliation(s)
- Tamas Varga
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Kim K. Hixson
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Amir H. Ahkami
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Andrew W. Sher
- School of Environmental and Forest Sciences, College of the Environment, University of Washington, Seattle, WA, United States
| | - Morgan E. Barnes
- Environmental Systems Graduate Group, University of California, Merced, Merced, CA, United States
| | - Rosalie K. Chu
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Anil K. Battu
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Carrie D. Nicora
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Tanya E. Winkler
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Loren R. Reno
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Sirine C. Fakra
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Olga Antipova
- Advanced Photon Source, Argonne National Laboratory, Lemont, IL, United States
| | - Dilworth Y. Parkinson
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Jackson R. Hall
- School of Environmental and Forest Sciences, College of the Environment, University of Washington, Seattle, WA, United States
| | - Sharon L. Doty
- School of Environmental and Forest Sciences, College of the Environment, University of Washington, Seattle, WA, United States
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