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Title: Top-down mass spectrometry of histone modifications in sorghum reveals potential epigenetic markers for drought acclimation

Abstract

Sorghum [Sorghum bicolor (L.) Moench] is an important cereal crop noted for its ability to survive water-limiting conditions. In this paper, we present an analytical workflow to explore the changes in histone modifications through plant developmental stages and two drought stresses in two sorghum genotypes that differ in their response to drought. Top-down mass spectrometry (MS) is an ideal method to profile histone modifications and distinguish closely related histone proteoforms. We analyzed leaves of 48 plants and identified 26 unique histone proteins and 677 unique histone proteoforms (124 full-length and 553 truncated proteoforms). We detected trimethylation on nearly all H2B N-termini where acetylation is commonly expected. In addition, an unexpected modification on H2A histones was assigned to N-pyruvic acid 2-iminylation based on its unique neutral loss of CO2. Interestingly, some of the truncated histones, in particular H4 and H3.2, showed significant changes that correlated with the growth and water conditions. Furthermore, the histone proteoforms could serve as targets in search of chromatin modifiers and ultimately have important ramifications in future attempts of studying plant epigenetic reprogramming under stress.

Authors:
ORCiD logo [1];  [1];  [1];  [1];  [1];  [2];  [2];  [2];  [3];  [4];  [4];  [1];  [1];  [1]
  1. Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Environmental Molecular Sciences Laboratory (EMSL)
  2. UC-ANR Kearney Agricultural Research & Extension Center, Parlier, CA (United States)
  3. Univ. of California, Davis, CA (United States)
  4. Univ. of California, Berkeley, CA (United States)
Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Environmental Molecular Sciences Lab. (EMSL); Univ. of California, Berkeley, CA (United States); Joint BioEnergy Institute (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER); USDA
OSTI Identifier:
1660761
Alternate Identifier(s):
OSTI ID: 1773357; OSTI ID: 1809705
Report Number(s):
PNNL-SA-145507
Journal ID: ISSN 1046-2023
Grant/Contract Number:  
SC0014081; AC02-05CH11231; AC05-76RL01830
Resource Type:
Accepted Manuscript
Journal Name:
Methods
Additional Journal Information:
Journal Volume: 184; Journal Issue: SI; Journal ID: ISSN 1046-2023
Publisher:
Elsevier
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Drought; Epigenetics; Histone clipping; Post-translational modifications; Sorghum; Top-down mass spectrometry

Citation Formats

Zhou, Mowei, Malhan, Neha, Ahkami, Amir H., Engbrecht, Kristin, Myers, Gabriel, Dahlberg, Jeffery, Hollingsworth, Joy, Sievert, Julie A., Hutmacher, Robert, Madera, Mary, Lemaux, Peggy G., Hixson, Kim K., Jansson, Christer, and Paša-Tolić, Ljiljana. Top-down mass spectrometry of histone modifications in sorghum reveals potential epigenetic markers for drought acclimation. United States: N. p., 2019. Web. doi:10.1016/j.ymeth.2019.10.007.
Zhou, Mowei, Malhan, Neha, Ahkami, Amir H., Engbrecht, Kristin, Myers, Gabriel, Dahlberg, Jeffery, Hollingsworth, Joy, Sievert, Julie A., Hutmacher, Robert, Madera, Mary, Lemaux, Peggy G., Hixson, Kim K., Jansson, Christer, & Paša-Tolić, Ljiljana. Top-down mass spectrometry of histone modifications in sorghum reveals potential epigenetic markers for drought acclimation. United States. https://doi.org/10.1016/j.ymeth.2019.10.007
Zhou, Mowei, Malhan, Neha, Ahkami, Amir H., Engbrecht, Kristin, Myers, Gabriel, Dahlberg, Jeffery, Hollingsworth, Joy, Sievert, Julie A., Hutmacher, Robert, Madera, Mary, Lemaux, Peggy G., Hixson, Kim K., Jansson, Christer, and Paša-Tolić, Ljiljana. Wed . "Top-down mass spectrometry of histone modifications in sorghum reveals potential epigenetic markers for drought acclimation". United States. https://doi.org/10.1016/j.ymeth.2019.10.007. https://www.osti.gov/servlets/purl/1660761.
@article{osti_1660761,
title = {Top-down mass spectrometry of histone modifications in sorghum reveals potential epigenetic markers for drought acclimation},
author = {Zhou, Mowei and Malhan, Neha and Ahkami, Amir H. and Engbrecht, Kristin and Myers, Gabriel and Dahlberg, Jeffery and Hollingsworth, Joy and Sievert, Julie A. and Hutmacher, Robert and Madera, Mary and Lemaux, Peggy G. and Hixson, Kim K. and Jansson, Christer and Paša-Tolić, Ljiljana},
abstractNote = {Sorghum [Sorghum bicolor (L.) Moench] is an important cereal crop noted for its ability to survive water-limiting conditions. In this paper, we present an analytical workflow to explore the changes in histone modifications through plant developmental stages and two drought stresses in two sorghum genotypes that differ in their response to drought. Top-down mass spectrometry (MS) is an ideal method to profile histone modifications and distinguish closely related histone proteoforms. We analyzed leaves of 48 plants and identified 26 unique histone proteins and 677 unique histone proteoforms (124 full-length and 553 truncated proteoforms). We detected trimethylation on nearly all H2B N-termini where acetylation is commonly expected. In addition, an unexpected modification on H2A histones was assigned to N-pyruvic acid 2-iminylation based on its unique neutral loss of CO2. Interestingly, some of the truncated histones, in particular H4 and H3.2, showed significant changes that correlated with the growth and water conditions. Furthermore, the histone proteoforms could serve as targets in search of chromatin modifiers and ultimately have important ramifications in future attempts of studying plant epigenetic reprogramming under stress.},
doi = {10.1016/j.ymeth.2019.10.007},
journal = {Methods},
number = SI,
volume = 184,
place = {United States},
year = {2019},
month = {10}
}

Journal Article:

Figures / Tables:

Fig. 1 Fig. 1: (a) Experimental design for studying the response of two sorghum genotypes to different watering conditions. Top panel shows the watering conditions and sample collection time points for histone analysis. The table shows the number of biological replicates (i.e. different plants) used. Some biological replicates were pooled to providemore » sufficient material for the analysis. (b) A representative LC-MS feature map of intact histones extracted from sorghum leaves. The 2D display plots the LC retention time vs. the mass for all detected proteoforms. The log abundance is coded by the color as shown by the scale in the top right corner. The major histone peaks are labeled by the dashed green boxes. The features outside the boxes are primarily truncated histones and ribosomal proteins. Zoom-in views of (c) H4, (d) H3, (e) H2B/16 kDa H2A, and (f) 14 kDa H2A feature maps in the same format as used for (b). Only major histone species are annotated with their PTMs. A complete list of identified histone proteoforms is presented in Table S1. In (e), all 16 kDa H2A species are denoted in green. In (f), the major 14 kDa H2A species (UniProt: C5XAT9) are denoted in green. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)« less

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Works referenced in this record:

The double face of the histone variant H3.3
journal, January 2011

  • Szenker, Emmanuelle; Ray-Gallet, Dominique; Almouzni, Geneviève
  • Cell Research, Vol. 21, Issue 3
  • DOI: 10.1038/cr.2011.14

The top-down, middle-down, and bottom-up mass spectrometry approaches for characterization of histone variants and their post-translational modifications
journal, December 2013

  • Moradian, Annie; Kalli, Anastasia; Sweredoski, Michael J.
  • PROTEOMICS, Vol. 14, Issue 4-5
  • DOI: 10.1002/pmic.201300256

Variations of Histone Modification Patterns: Contributions of Inter-plant Variability and Technical Factors
journal, December 2017

  • Brabencová, Sylva; Ihnatová, Ivana; Potěšil, David
  • Frontiers in Plant Science, Vol. 8
  • DOI: 10.3389/fpls.2017.02084

The First Identification of Lysine Malonylation Substrates and Its Regulatory Enzyme
journal, September 2011

  • Peng, Chao; Lu, Zhike; Xie, Zhongyu
  • Molecular & Cellular Proteomics, Vol. 10, Issue 12
  • DOI: 10.1074/mcp.M111.012658

iTop-Q: an Intelligent Tool for Top-down Proteomics Quantitation Using DYAMOND Algorithm
journal, December 2017


Histone variants on the move: substrates for chromatin dynamics
journal, December 2016

  • Talbert, Paul B.; Henikoff, Steven
  • Nature Reviews Molecular Cell Biology, Vol. 18, Issue 2
  • DOI: 10.1038/nrm.2016.148

Quantitative Proteomic Analysis of Histone Modifications
journal, October 2014

  • Huang, He; Lin, Shu; Garcia, Benjamin A.
  • Chemical Reviews, Vol. 115, Issue 6
  • DOI: 10.1021/cr500491u

Epigenetic Regulation in Plant Responses to the Environment
journal, September 2014


The PRIDE database and related tools and resources in 2019: improving support for quantification data
journal, November 2018

  • Perez-Riverol, Yasset; Csordas, Attila; Bai, Jingwen
  • Nucleic Acids Research, Vol. 47, Issue D1
  • DOI: 10.1093/nar/gky1106

Sorghum bicolor — an important species for comparative grass genomics and a source of beneficial genes for agriculture
journal, April 2002


The conformational flexibility of the C-terminus of histone H4 promotes histone octamer and nucleosome stability and yeast viability
journal, January 2012

  • Chavez, Myrriah S.; Scorgie, Jean K.; Dennehey, Briana K.
  • Epigenetics & Chromatin, Vol. 5, Issue 1
  • DOI: 10.1186/1756-8935-5-5

pTop 1.0: A High-Accuracy and High-Efficiency Search Engine for Intact Protein Identification
journal, February 2016


Identification and Quantification of Proteoforms by Mass Spectrometry
journal, May 2019

  • Schaffer, Leah V.; Millikin, Robert J.; Miller, Rachel M.
  • PROTEOMICS, Vol. 19, Issue 10
  • DOI: 10.1002/pmic.201800361

Decoding protein modifications using top-down mass spectrometry
journal, September 2007

  • Siuti, Nertila; Kelleher, Neil L.
  • Nature Methods, Vol. 4, Issue 10
  • DOI: 10.1038/nmeth1097

Profiling of Histone Post-Translational Modifications in Mouse Brain with High-Resolution Top-Down Mass Spectrometry
journal, December 2016


Characterization of Post-Translational Modifications of Histone H2B-Variants Isolated from Arabidopsis thaliana
journal, September 2007

  • Bergmüller, Eveline; Gehrig, Peter M.; Gruissem, Wilhelm
  • Journal of Proteome Research, Vol. 6, Issue 9
  • DOI: 10.1021/pr0702159

N-Trimethylalanine, a Novel Blocked N-Terminal Residue of Tetrahymena Histone H2B1
journal, October 1982


A Conserved Patch near the C Terminus of Histone H4 Is Required for Genome Stability in Budding Yeast
journal, March 2011

  • Yu, Y.; Srinivasan, M.; Nakanishi, S.
  • Molecular and Cellular Biology, Vol. 31, Issue 11
  • DOI: 10.1128/MCB.01432-10

Clipping of Flexible Tails of Histones H3 and H4 Affects the Structure and Dynamics of the Nucleosome
journal, March 2013

  • Nurse, Nathan P.; Jimenez-Useche, Isabel; Smith, Ian Tad
  • Biophysical Journal, Vol. 104, Issue 5
  • DOI: 10.1016/j.bpj.2013.01.019

Strong succession in arbuscular mycorrhizal fungal communities
journal, August 2018


The C-Score: A Bayesian Framework to Sharply Improve Proteoform Scoring in High-Throughput Top Down Proteomics
journal, June 2014

  • LeDuc, Richard D.; Fellers, Ryan T.; Early, Bryan P.
  • Journal of Proteome Research, Vol. 13, Issue 7
  • DOI: 10.1021/pr401277r

Water-use efficiency of sweet sorghum under water stress conditions Gas-exchange investigations at leaf and canopy scales
journal, September 1997


Increasing the Separation Capacity of Intact Histone Proteoforms Chromatography Coupling Online Weak Cation Exchange-HILIC to Reversed Phase LC UVPD-HRMS
journal, September 2018


Enhanced top-down characterization of histone post-translational modifications
journal, January 2012


Histones of Chlamydomonas reinhardtii (Synthesis, Acetylation, and Methylation)
journal, October 1995

  • Waterborg, J. H.; Robertson, A. J.; Tatar, D. L.
  • Plant Physiology, Vol. 109, Issue 2
  • DOI: 10.1104/pp.109.2.393

Targeting the cancer epigenome for therapy
journal, September 2016

  • Jones, Peter A.; Issa, Jean-Pierre J.; Baylin, Stephen
  • Nature Reviews Genetics, Vol. 17, Issue 10
  • DOI: 10.1038/nrg.2016.93

Unabridged Analysis of Human Histone H3 by Differential Top-Down Mass Spectrometry Reveals Hypermethylated Proteoforms from MMSET/NSD2 Overexpression
journal, March 2016

  • Zheng, Yupeng; Fornelli, Luca; Compton, Philip D.
  • Molecular & Cellular Proteomics, Vol. 15, Issue 3
  • DOI: 10.1074/mcp.M115.053819

Mass spectrometry analysis of the variants of histone H3 and H4 of soybean and their post-translational modifications
journal, January 2009


Informed-Proteomics: open-source software package for top-down proteomics
journal, August 2017

  • Park, Jungkap; Piehowski, Paul D.; Wilkins, Christopher
  • Nature Methods, Vol. 14, Issue 9
  • DOI: 10.1038/nmeth.4388

Native GELFrEE: A New Separation Technique for Biomolecular Assemblies
journal, February 2015

  • Skinner, Owen S.; Do Vale, Luis H. F.; Catherman, Adam D.
  • Analytical Chemistry, Vol. 87, Issue 5
  • DOI: 10.1021/ac504678d

Role of glutathione in the regulation of epigenetic mechanisms in disease
journal, November 2017


Identification of Protein N-Terminal Methyltransferases in Yeast and Humans
journal, June 2010

  • Webb, Kristofor J.; Lipson, Rebecca S.; Al-Hadid, Qais
  • Biochemistry, Vol. 49, Issue 25
  • DOI: 10.1021/bi100428x

Drought under global warming: a review: Drought under global warming
journal, October 2010

  • Dai, Aiguo
  • Wiley Interdisciplinary Reviews: Climate Change, Vol. 2, Issue 1
  • DOI: 10.1002/wcc.81

Mass Spectrometric Quantification of Histone Post-translational Modifications by a Hybrid Chemical Labeling Method
journal, February 2015

  • Maile, Tobias M.; Izrael-Tomasevic, Anita; Cheung, Tommy
  • Molecular & Cellular Proteomics, Vol. 14, Issue 4
  • DOI: 10.1074/mcp.O114.046573

Progress in Top-Down Proteomics and the Analysis of Proteoforms
journal, June 2016


Understanding the complex nature of salinity and drought-stress response in cereals using proteomics technologies
journal, March 2014


SnapShot: Histone Modifications
journal, October 2014


Analyses of Histone Proteoforms Using Front-end Electron Transfer Dissociation-enabled Orbitrap Instruments
journal, March 2016

  • Anderson, Lissa C.; Karch, Kelly R.; Ugrin, Scott A.
  • Molecular & Cellular Proteomics, Vol. 15, Issue 3
  • DOI: 10.1074/mcp.O115.053843

Histone proteolysis: A proposal for categorization into ‘clipping’ and ‘degradation’: Prospects & Overviews
journal, October 2014


Multi-faceted quantitative proteomics analysis of histone H2B isoforms and their modifications
journal, April 2015

  • Molden, Rosalynn C.; Bhanu, Natarajan V.; LeRoy, Gary
  • Epigenetics & Chromatin, Vol. 8, Issue 1
  • DOI: 10.1186/s13072-015-0006-8

Top-Down Proteomics of Large Proteins up to 223 kDa Enabled by Serial Size Exclusion Chromatography Strategy
journal, April 2017


Histone H3 variants and their potential role in indexing mammalian genomes: The "H3 barcode hypothesis"
journal, March 2006

  • Hake, S. B.; Allis, C. D.
  • Proceedings of the National Academy of Sciences, Vol. 103, Issue 17
  • DOI: 10.1073/pnas.0600803103

Genetic Engineering and Water
journal, June 2001


Drought delays development of the sorghum root microbiome and enriches for monoderm bacteria
journal, April 2018

  • Xu, Ling; Naylor, Dan; Dong, Zhaobin
  • Proceedings of the National Academy of Sciences, Vol. 115, Issue 18
  • DOI: 10.1073/pnas.1717308115

Top-down protein identification using isotopic envelope fingerprinting
journal, January 2017


Heavy Sugar and Heavy Water Create Tunable Intact Protein Mass Increases for Quantitative Mass Spectrometry in Any Feed and Organism
journal, October 2016

  • Quijada, Jeniffer V.; Schmitt, Nicholas D.; Salisbury, Joseph P.
  • Analytical Chemistry, Vol. 88, Issue 22
  • DOI: 10.1021/acs.analchem.6b03234

Applying Label-Free Quantitation to Top Down Proteomics
journal, May 2014

  • Ntai, Ioanna; Kim, Kyunggon; Fellers, Ryan T.
  • Analytical Chemistry, Vol. 86, Issue 10
  • DOI: 10.1021/ac500395k

Structural Diversity of Nucleosomes Characterized by Native Mass Spectrometry
journal, May 2018


Histone Variant H3.3: A versatile H3 variant in health and in disease
journal, January 2016


Designing sorghum as a dedicated bioenergy feedstock
journal, October 2007

  • Rooney, William L.; Blumenthal, Jürg; Bean, Brent
  • Biofuels, Bioproducts and Biorefining, Vol. 1, Issue 2
  • DOI: 10.1002/bbb.15

Molecular basis for histone N-terminal methylation by NRMT1
journal, November 2015


A New Approach for Plant Proteomics
journal, December 2003

  • Zabrouskov, Vlad; Giacomelli, Lisa; van Wijk, Klaas J.
  • Molecular & Cellular Proteomics, Vol. 2, Issue 12
  • DOI: 10.1074/mcp.M300069-MCP200

Top-down quantitation and characterization of SILAC-labeled proteins
journal, November 2007

  • Waanders, Leonie F.; Hanke, Stefan; Mann, Matthias
  • Journal of the American Society for Mass Spectrometry, Vol. 18, Issue 11
  • DOI: 10.1016/j.jasms.2007.09.001

Distinctive Core Histone Post-Translational Modification Patterns in Arabidopsis thaliana
journal, November 2007


Analysis of Histones H3 and H4 Reveals Novel and Conserved Post-Translational Modifications in Sugarcane
journal, July 2015


Nucleosome Structure and Function
journal, October 2014

  • McGinty, Robert K.; Tan, Song
  • Chemical Reviews, Vol. 115, Issue 6
  • DOI: 10.1021/cr500373h

Tandem Mass Tag Protein Labeling for Top-Down Identification and Quantification
journal, December 2011

  • Hung, Chien-Wen; Tholey, Andreas
  • Analytical Chemistry, Vol. 84, Issue 1
  • DOI: 10.1021/ac202243r

Are neutral loss and internal product ions useful for top-down protein identification?
journal, May 2017


Regulation of nucleosome dynamics by histone modifications
journal, March 2013

  • Zentner, Gabriel E.; Henikoff, Steven
  • Nature Structural & Molecular Biology, Vol. 20, Issue 3
  • DOI: 10.1038/nsmb.2470

Protein N-terminal methionine excision
journal, June 2004

  • Giglione, C.; Boularot, A.; Meinnel, T.
  • Cellular and Molecular Life Sciences, Vol. 61, Issue 12
  • DOI: 10.1007/s00018-004-3466-8

Lysine Succinylation and Lysine Malonylation in Histones
journal, March 2012

  • Xie, Zhongyu; Dai, Junbiao; Dai, Lunzhi
  • Molecular & Cellular Proteomics, Vol. 11, Issue 5
  • DOI: 10.1074/mcp.M111.015875

Top-down high-resolution mass spectrometry of cardiac myosin binding protein C revealed that truncation alters protein phosphorylation state
journal, June 2009

  • Ge, Y.; Rybakova, I. N.; Xu, Q.
  • Proceedings of the National Academy of Sciences, Vol. 106, Issue 31
  • DOI: 10.1073/pnas.0813369106

N-terminal methylation of proteins: Structure, function and specificity
journal, August 1987


Histones and histone genes in higher plants: Structure and genomic organization
journal, January 1993


MASH Suite Pro: A Comprehensive Software Tool for Top-Down Proteomics
journal, November 2015

  • Cai, Wenxuan; Guner, Huseyin; Gregorich, Zachery R.
  • Molecular & Cellular Proteomics, Vol. 15, Issue 2
  • DOI: 10.1074/mcp.O115.054387

Molecular implementation and physiological roles for histone H3 lysine 4 (H3K4) methylation
journal, June 2008


Two-dimensional separation using high-pH and low-pH reversed phase liquid chromatography for top-down proteomics
journal, April 2018


Identification of five sites of acetylation in alfalfa histone H4
journal, July 1992


Top-down/Bottom-up Mass Spectrometry Workflow Using Dissolvable Polyacrylamide Gels
journal, July 2017


Top-down and Middle-down Protein Analysis Reveals that Intact and Clipped Human Histones Differ in Post-translational Modification Patterns*
journal, December 2015

  • Tvardovskiy, Andrey; Wrzesinski, Krzysztof; Sidoli, Simone
  • Molecular & Cellular Proteomics, Vol. 14, Issue 12
  • DOI: 10.1074/mcp.M115.048975

Intact Protein Quantitation Using Pseudoisobaric Dimethyl Labeling
journal, July 2016


Plant Proteases: From Phenotypes to Molecular Mechanisms
journal, June 2008


Histone H3 Glutathionylation in Proliferating Mammalian Cells Destabilizes Nucleosomal Structure
journal, October 2013

  • García-Giménez, José Luis; Olaso, Gloria; Hake, Sandra B.
  • Antioxidants & Redox Signaling, Vol. 19, Issue 12
  • DOI: 10.1089/ars.2012.5021

N-terminal modifications of cellular proteins: The enzymes involved, their substrate specificities and biological effects
journal, June 2015


Proteolytic clipping of histone tails: the emerging role of histone proteases in regulation of various biological processes
journal, January 2014


Involvement of Histone Modifications in Plant Abiotic Stress Responses: Histone Modifications in Plant Abiotic Stress Responses
journal, August 2013

  • Yuan, Lianyu; Liu, Xuncheng; Luo, Ming
  • Journal of Integrative Plant Biology, Vol. 55, Issue 10
  • DOI: 10.1111/jipb.12060

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