Discovery top-down proteomics in symbiotic soybean root nodules
Abstract
Proteomic methods have been widely used to study proteins in complex biological samples to understand biological molecular mechanisms. Most well-established methods (known as bottom-up proteomics, BUP) employ an enzymatic digestion step to cleave intact proteins into smaller peptides for liquid chromatography (LC) mass spectrometry (MS) detection. In contrast, top-down proteomics (TDP) directly characterizes intact proteins including all possible post-translational modifications (PTMs), thus offering unique insights into proteoform biology where combinations of individual PTMs may play important roles. We performed TDP on soybean root nodules infected by the symbiotic Bradyrhizobium japonicum in both the wildtype bacterium and a nifH- mutant, which lacks the ability to fix nitrogen in the soybean root nodule. TDP captured 1648 proteoforms derived from 313 bacterial genes and 178 soybean genes. Leghemoglobin, the most abundant protein in the sample, existed in many truncated proteoforms. Interestingly, these truncated proteoforms were considerably more abundant in the wildtype relative to the nifH- mutant, implicating protease activity as an important factor in nitrogen fixation. Proteoforms with various PTMs and combinations thereof were identified using an unrestricted open modification search. This included less common PTMs such as myristoylation, palmitoylation, cyanylation, and sulfation. In parallel, we collected high resolution MS imaging (MSI) datamore »
- Authors:
- Publication Date:
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1890547
- Grant/Contract Number:
- 10.46936/lser.proj. 2021.51846/60000343 10.46936/intm.proj. 2020.51671/60000250 10.46936/intm.proj. 2019.51159/60000152
- Resource Type:
- Published Article
- Journal Name:
- Frontiers in Analytical Science
- Additional Journal Information:
- Journal Name: Frontiers in Analytical Science Journal Volume: 2; Journal ID: ISSN 2673-9283
- Publisher:
- Frontiers Media SA
- Country of Publication:
- Switzerland
- Language:
- English
Citation Formats
Zhou, Mowei, Fulcher, James M., Zemaitis, Kevin J., Degnan, David J., Liao, Yen-Chen, Veličković, Marija, Veličković, Dušan, Bramer, Lisa M., Kew, William R., Stacey, Gary, and Paša-Tolić, Ljiljana. Discovery top-down proteomics in symbiotic soybean root nodules. Switzerland: N. p., 2022.
Web. doi:10.3389/frans.2022.1012707.
Zhou, Mowei, Fulcher, James M., Zemaitis, Kevin J., Degnan, David J., Liao, Yen-Chen, Veličković, Marija, Veličković, Dušan, Bramer, Lisa M., Kew, William R., Stacey, Gary, & Paša-Tolić, Ljiljana. Discovery top-down proteomics in symbiotic soybean root nodules. Switzerland. https://doi.org/10.3389/frans.2022.1012707
Zhou, Mowei, Fulcher, James M., Zemaitis, Kevin J., Degnan, David J., Liao, Yen-Chen, Veličković, Marija, Veličković, Dušan, Bramer, Lisa M., Kew, William R., Stacey, Gary, and Paša-Tolić, Ljiljana. Fri .
"Discovery top-down proteomics in symbiotic soybean root nodules". Switzerland. https://doi.org/10.3389/frans.2022.1012707.
@article{osti_1890547,
title = {Discovery top-down proteomics in symbiotic soybean root nodules},
author = {Zhou, Mowei and Fulcher, James M. and Zemaitis, Kevin J. and Degnan, David J. and Liao, Yen-Chen and Veličković, Marija and Veličković, Dušan and Bramer, Lisa M. and Kew, William R. and Stacey, Gary and Paša-Tolić, Ljiljana},
abstractNote = {Proteomic methods have been widely used to study proteins in complex biological samples to understand biological molecular mechanisms. Most well-established methods (known as bottom-up proteomics, BUP) employ an enzymatic digestion step to cleave intact proteins into smaller peptides for liquid chromatography (LC) mass spectrometry (MS) detection. In contrast, top-down proteomics (TDP) directly characterizes intact proteins including all possible post-translational modifications (PTMs), thus offering unique insights into proteoform biology where combinations of individual PTMs may play important roles. We performed TDP on soybean root nodules infected by the symbiotic Bradyrhizobium japonicum in both the wildtype bacterium and a nifH- mutant, which lacks the ability to fix nitrogen in the soybean root nodule. TDP captured 1648 proteoforms derived from 313 bacterial genes and 178 soybean genes. Leghemoglobin, the most abundant protein in the sample, existed in many truncated proteoforms. Interestingly, these truncated proteoforms were considerably more abundant in the wildtype relative to the nifH- mutant, implicating protease activity as an important factor in nitrogen fixation. Proteoforms with various PTMs and combinations thereof were identified using an unrestricted open modification search. This included less common PTMs such as myristoylation, palmitoylation, cyanylation, and sulfation. In parallel, we collected high resolution MS imaging (MSI) data of intact proteins and biopolymers (<20 kDa due to current technical limitations) from sections of the soybean root nodules using matrix-assisted laser desorption/ionization (MALDI) coupled to high resolution Orbitrap. Several detected proteoforms exhibited unique spatial distributions inside the infection zone and cortex, suggesting functional compartmentalization in these regions. A subset of peaks from the MALDI-MSI were assigned to proteoforms detected in TDP LCMS data based on matching accurate masses. Many of the proteins detected in both LCMS and MALDI-MSI are currently uncharacterized in UniProt: the PTM and spatial information presented here will be valuable in understanding their biological functions. Taken together, our study demonstrates how untargeted TDP approach can provide unique insights into plant proteoform biology. On-going technology developments are expected to further improve TDP coverage for more comprehensive high-throughput analysis of proteoforms.},
doi = {10.3389/frans.2022.1012707},
journal = {Frontiers in Analytical Science},
number = ,
volume = 2,
place = {Switzerland},
year = {Fri Sep 30 00:00:00 EDT 2022},
month = {Fri Sep 30 00:00:00 EDT 2022}
}
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