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Title: Soybean Roots Grown under Heat Stress Show Global Changes in Their Transcriptional and Proteomic Profiles

Abstract

Heat stress is likely to be a key factor in the negative impact of climate change on crop production. Heat stress significantly influences the functions of roots, which provide support, water, and nutrients to other plant organs. Likewise, roots play an important role in the establishment of symbiotic associations with different microorganisms. Despite the physiological relevance of roots, few studies have examined their response to heat stress. Here in this study, we performed genome-wide transcriptomic and proteomic analyses on isolated root hairs, which are a single, epidermal cell type, and compared their response to stripped roots. On average, we identified 1849 and 3091 genes differentially regulated in root hairs and stripped roots, respectively, in response to heat stress. Our gene regulatory module analysis identified 10 key modules that might control the majority of the transcriptional response to heat stress. We also conducted proteomic analysis on membrane fractions isolated from root hairs and compared these responses to stripped roots. These experiments identified a variety of proteins whose expression changed within 3 h of application of heat stress. Most of these proteins were predicted to play a significant role in thermo-tolerance, as well as in chromatin remodeling and post-transcriptional regulation. In conclusion,more » the data presented represent an in-depth analysis of the heat stress response of a single cell type in soybean.« less

Authors:
 [1];  [2];  [2];  [2];  [3];  [4];  [5];  [6];  [7];  [7];  [7];  [7];  [2]
  1. Univ. of Missouri, Columbia, MO (United States). National Center for Soybean Biotechnology, C.S. Bond Life Sciences Center, Division of Plant Sciences and Biochemistry; Univ. Nacional Autonoma de Mexico (UNAM), Mexico City (Mexico). Lab. de Genomica Funcional de Leguminosas, Facultad de Estudios Superiores Iztacala
  2. Univ. of Missouri, Columbia, MO (United States). National Center for Soybean Biotechnology, C.S. Bond Life Sciences Center, Division of Plant Sciences and Biochemistry
  3. Univ. Nacional Autonoma de Mexico (UNAM), Mexico City (Mexico). Lab. de Genomica Funcional de Leguminosas, Facultad de Estudios Superiores Iztacalav
  4. Univ. of Missouri, Columbia, MO (United States). C.S. Bond Life Sciences Center, Informatics Inst.
  5. Univ. of Missouri, Columbia, MO (United States). C.S. Bond Life Sciences Center, Informatics Inst.; Univ. of Missouri, Columbia, MO (United States). Dept. of Computer Science; Univ. of Missouri, Columbia, MO (United States). School of Medicine, Dept. of Molecular Microbiology and Immunology and Office of Research
  6. Univ. of Missouri, Columbia, MO (United States). C.S. Bond Life Sciences Center, Informatics Inst.; Univ. of Missouri, Columbia, MO (United States). Dept. of Computer Science
  7. Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Environmental Molecular Sciences Lab. (EMSL)
Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE Office of Science (SC); USDOE Laboratory Directed Research and Development (LDRD) Program
OSTI Identifier:
1357046
Report Number(s):
PNNL-SA-114787
Journal ID: ISSN 1664-462X
Grant/Contract Number:  
SC0004898; AC05-76RL01830; 219759; 252260; IA203815; FESI-DIP-PAPCA-2014-3
Resource Type:
Accepted Manuscript
Journal Name:
Frontiers in Plant Science
Additional Journal Information:
Journal Volume: 7; Journal ID: ISSN 1664-462X
Publisher:
Frontiers Research Foundation
Country of Publication:
United States
Language:
English
Subject:
54 ENVIRONMENTAL SCIENCES; 59 BASIC BIOLOGICAL SCIENCES; soybean; roothairs; heatstress; genemodule; transcriptomics; proteomics

Citation Formats

Valdés-López, Oswaldo, Batek, Josef, Gomez-Hernandez, Nicolas, Nguyen, Cuong T., Isidra-Arellano, Mariel C., Zhang, Ning, Joshi, Trupti, Xu, Dong, Hixson, Kim K., Weitz, Karl K., Aldrich, Joshua T., Paša-Tolić, Ljiljana, and Stacey, Gary. Soybean Roots Grown under Heat Stress Show Global Changes in Their Transcriptional and Proteomic Profiles. United States: N. p., 2016. Web. doi:10.3389/fpls.2016.00517.
Valdés-López, Oswaldo, Batek, Josef, Gomez-Hernandez, Nicolas, Nguyen, Cuong T., Isidra-Arellano, Mariel C., Zhang, Ning, Joshi, Trupti, Xu, Dong, Hixson, Kim K., Weitz, Karl K., Aldrich, Joshua T., Paša-Tolić, Ljiljana, & Stacey, Gary. Soybean Roots Grown under Heat Stress Show Global Changes in Their Transcriptional and Proteomic Profiles. United States. doi:10.3389/fpls.2016.00517.
Valdés-López, Oswaldo, Batek, Josef, Gomez-Hernandez, Nicolas, Nguyen, Cuong T., Isidra-Arellano, Mariel C., Zhang, Ning, Joshi, Trupti, Xu, Dong, Hixson, Kim K., Weitz, Karl K., Aldrich, Joshua T., Paša-Tolić, Ljiljana, and Stacey, Gary. Mon . "Soybean Roots Grown under Heat Stress Show Global Changes in Their Transcriptional and Proteomic Profiles". United States. doi:10.3389/fpls.2016.00517. https://www.osti.gov/servlets/purl/1357046.
@article{osti_1357046,
title = {Soybean Roots Grown under Heat Stress Show Global Changes in Their Transcriptional and Proteomic Profiles},
author = {Valdés-López, Oswaldo and Batek, Josef and Gomez-Hernandez, Nicolas and Nguyen, Cuong T. and Isidra-Arellano, Mariel C. and Zhang, Ning and Joshi, Trupti and Xu, Dong and Hixson, Kim K. and Weitz, Karl K. and Aldrich, Joshua T. and Paša-Tolić, Ljiljana and Stacey, Gary},
abstractNote = {Heat stress is likely to be a key factor in the negative impact of climate change on crop production. Heat stress significantly influences the functions of roots, which provide support, water, and nutrients to other plant organs. Likewise, roots play an important role in the establishment of symbiotic associations with different microorganisms. Despite the physiological relevance of roots, few studies have examined their response to heat stress. Here in this study, we performed genome-wide transcriptomic and proteomic analyses on isolated root hairs, which are a single, epidermal cell type, and compared their response to stripped roots. On average, we identified 1849 and 3091 genes differentially regulated in root hairs and stripped roots, respectively, in response to heat stress. Our gene regulatory module analysis identified 10 key modules that might control the majority of the transcriptional response to heat stress. We also conducted proteomic analysis on membrane fractions isolated from root hairs and compared these responses to stripped roots. These experiments identified a variety of proteins whose expression changed within 3 h of application of heat stress. Most of these proteins were predicted to play a significant role in thermo-tolerance, as well as in chromatin remodeling and post-transcriptional regulation. In conclusion, the data presented represent an in-depth analysis of the heat stress response of a single cell type in soybean.},
doi = {10.3389/fpls.2016.00517},
journal = {Frontiers in Plant Science},
number = ,
volume = 7,
place = {United States},
year = {2016},
month = {4}
}

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Works referenced in this record:

A Two-Stage Poisson Model for Testing RNA-Seq Data
journal, January 2011

  • Auer, Paul L.; Doerge, Rebecca W.
  • Statistical Applications in Genetics and Molecular Biology, Vol. 10, Issue 1
  • DOI: 10.2202/1544-6115.1627

Genome scale transcriptional response diversity among ten ecotypes of Arabidopsis thaliana during heat stress
journal, January 2013


The complex language of chromatin regulation during transcription
journal, May 2007


Sex-specific and lineage-specific alternative splicing in primates
journal, December 2009


Establishment of a Protein Reference Map for Soybean Root Hair Cells
journal, November 2008

  • Brechenmacher, Laurent; Lee, Joohyun; Sachdev, Sherri
  • Plant Physiology, Vol. 149, Issue 2
  • DOI: 10.1104/pp.108.131649

Control of leghaemoglobin synthesis in snake beans
journal, December 1971

  • Broughton, W. J.; Dilworth, M. J.
  • Biochemical Journal, Vol. 125, Issue 4
  • DOI: 10.1042/bj1251075

Genome-wide identification and expression analysis of heat-responsive and novel microRNAs in Populus tomentosa
journal, August 2012


agriGO: a GO analysis toolkit for the agricultural community
journal, April 2010

  • Du, Zhou; Zhou, Xin; Ling, Yi
  • Nucleic Acids Research, Vol. 38, Issue suppl_2
  • DOI: 10.1093/nar/gkq310

Transcriptional networks — crops, clocks, and abiotic stress
journal, April 2015

  • Gehan, Malia A.; Greenham, Kathleen; Mockler, Todd C.
  • Current Opinion in Plant Biology, Vol. 24
  • DOI: 10.1016/j.pbi.2015.01.004

Fast and Accurate Database Searches with MS-GF+Percolator
journal, December 2013

  • Granholm, Viktor; Kim, Sangtae; Navarro, José C. F.
  • Journal of Proteome Research, Vol. 13, Issue 2
  • DOI: 10.1021/pr400937n

Heat stress induction of miR398 triggers a regulatory loop that is critical for thermotolerance in Arabidopsis
journal, April 2013

  • Guan, Qingmei; Lu, Xiaoyan; Zeng, Haitao
  • The Plant Journal, Vol. 74, Issue 5
  • DOI: 10.1111/tpj.12169

Crops that feed the World 2. Soybean—worldwide production, use, and constraints caused by pathogens and pests
journal, January 2011


Physiological, Biochemical, and Molecular Mechanisms of Heat Stress Tolerance in Plants
journal, May 2013

  • Hasanuzzaman, Mirza; Nahar, Kamrun; Alam, Md.
  • International Journal of Molecular Sciences, Vol. 14, Issue 5
  • DOI: 10.3390/ijms14059643

System approaches to study root hairs as a single cell plant model: current status and future perspectives
journal, May 2015

  • Hossain, Md Shakhawat; Joshi, Trupti; Stacey, Gary
  • Frontiers in Plant Science, Vol. 6
  • DOI: 10.3389/fpls.2015.00363

Transcriptomic analysis of Sorghum bicolor responding to combined heat and drought stress
journal, January 2014


Soybean knowledge base (SoyKB): a web resource for integration of soybean translational genomics and molecular breeding
journal, October 2013

  • Joshi, Trupti; Fitzpatrick, Michael R.; Chen, Shiyuan
  • Nucleic Acids Research, Vol. 42, Issue D1
  • DOI: 10.1093/nar/gkt905

Soybean Knowledge Base (SoyKB): a web resource for soybean translational genomics
journal, January 2012


Chemically Etched Open Tubular and Monolithic Emitters for Nanoelectrospray Ionization Mass Spectrometry
journal, November 2006

  • Kelly, Ryan T.; Page, Jason S.; Luo, Quanzhou
  • Analytical Chemistry, Vol. 78, Issue 22, p. 7796-7801
  • DOI: 10.1021/ac061133r

MicroRNAs as regulators of root development and architecture
journal, May 2011

  • Khan, Ghazanfar A.; Declerck, Marie; Sorin, Céline
  • Plant Molecular Biology, Vol. 77, Issue 1-2
  • DOI: 10.1007/s11103-011-9793-x

Spectral Probabilities and Generating Functions of Tandem Mass Spectra: A Strike against Decoy Databases
journal, August 2008

  • Kim, Sangtae; Gupta, Nitin; Pevzner, Pavel A.
  • Journal of Proteome Research, Vol. 7, Issue 8
  • DOI: 10.1021/pr8001244

The Generating Function of CID, ETD, and CID/ETD Pairs of Tandem Mass Spectra: Applications to Database Search
journal, September 2010

  • Kim, Sangtae; Mischerikow, Nikolai; Bandeira, Nuno
  • Molecular & Cellular Proteomics, Vol. 9, Issue 12
  • DOI: 10.1074/mcp.M110.003731

H2A.Z-Containing Nucleosomes Mediate the Thermosensory Response in Arabidopsis
journal, January 2010


Heat Stress Phenotypes of Arabidopsis Mutants Implicate Multiple Signaling Pathways in the Acquisition of Thermotolerance
journal, May 2005

  • Larkindale, Jane; Hall, Jennifer D.; Knight, Marc R.
  • Plant Physiology, Vol. 138, Issue 2
  • DOI: 10.1104/pp.105.062257

Role of DREBs in regulation of abiotic stress responses in plants
journal, July 2011

  • Lata, C.; Prasad, M.
  • Journal of Experimental Botany, Vol. 62, Issue 14
  • DOI: 10.1093/jxb/err210

Comparative analysis of drought-responsive transcriptome in Indica rice genotypes with contrasting drought tolerance: Drought-responsive transcriptome analysis in rice
journal, August 2010


Transcriptome analysis of heat stress response in switchgrass (Panicum virgatum L.)
journal, January 2013


Complete Transcriptome of the Soybean Root Hair Cell, a Single-Cell Model, and Its Alteration in Response to Bradyrhizobium japonicum Infection
journal, November 2009

  • Libault, Marc; Farmer, Andrew; Brechenmacher, Laurent
  • Plant Physiology, Vol. 152, Issue 2
  • DOI: 10.1104/pp.109.148379

Identification of Four Soybean Reference Genes for Gene Expression Normalization
journal, January 2008


Differential proteomic analysis of grapevine leaves by iTRAQ reveals responses to heat stress and subsequent recovery
journal, January 2014


Genome-Wide Analyses of Early Translational Responses to Elevated Temperature and High Salinity in Arabidopsis thaliana
journal, January 2010

  • Matsuura, Hideyuki; Ishibashi, Yu; Shinmyo, Atsuhiko
  • Plant and Cell Physiology, Vol. 51, Issue 3
  • DOI: 10.1093/pcp/pcq010

Temperature-regulation of plant architecture
journal, July 2009

  • Patel, Dhaval; Franklin, Keara A.
  • Plant Signaling & Behavior, Vol. 4, Issue 7
  • DOI: 10.4161/psb.4.7.8849

Stress-Induced Chromatin Changes: A Critical View on Their Heritability
journal, March 2012

  • Pecinka, A.; Mittelsten Scheid, O.
  • Plant and Cell Physiology, Vol. 53, Issue 5
  • DOI: 10.1093/pcp/pcs044

The protein expression landscape of the Arabidopsis root
journal, March 2012

  • Petricka, J. J.; Schauer, M. A.; Megraw, M.
  • Proceedings of the National Academy of Sciences, Vol. 109, Issue 18
  • DOI: 10.1073/pnas.1202546109

Correlation of mRNA and protein abundance in the developing maize leaf
journal, April 2014

  • Ponnala, Lalit; Wang, Yupeng; Sun, Qi
  • The Plant Journal, Vol. 78, Issue 3
  • DOI: 10.1111/tpj.12482

Responses of tree fine roots to temperature: REVIEW Responses of fine roots to temperature
journal, July 2000


Molecular mechanisms of the plant heat stress response
journal, March 2013

  • Qu, Ai-Li; Ding, Yan-Fei; Jiang, Qiong
  • Biochemical and Biophysical Research Communications, Vol. 432, Issue 2
  • DOI: 10.1016/j.bbrc.2013.01.104

Assumption-free analysis of quantitative real-time polymerase chain reaction (PCR) data
journal, March 2003

  • Ramakers, Christian; Ruijter, Jan M.; Deprez, Ronald H. Lekanne
  • Neuroscience Letters, Vol. 339, Issue 1, p. 62-66
  • DOI: 10.1016/S0304-3940(02)01423-4

WRKY transcription factors
journal, May 2010


Coexpression network analysis associated with call of rice seedlings for encountering heat stress
journal, August 2013


Genome sequence of the palaeopolyploid soybean
journal, January 2010

  • Schmutz, Jeremy; Cannon, Steven B.; Schlueter, Jessica
  • Nature, Vol. 463, Issue 7278
  • DOI: 10.1038/nature08670

Statistical significance for genomewide studies
journal, July 2003

  • Storey, J. D.; Tibshirani, R.
  • Proceedings of the National Academy of Sciences, Vol. 100, Issue 16, p. 9440-9445
  • DOI: 10.1073/pnas.1530509100

Mapping and Dynamics of Regulatory DNA and Transcription Factor Networks in A. thaliana
journal, September 2014


mapman: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes
journal, March 2004


TopHat: discovering splice junctions with RNA-Seq
journal, March 2009


Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
journal, March 2012


Crop and pasture response to climate change
journal, December 2007

  • Tubiello, F. N.; Soussana, J. -F.; Howden, S. M.
  • Proceedings of the National Academy of Sciences, Vol. 104, Issue 50
  • DOI: 10.1073/pnas.0701728104

A guide to using MapMan to visualize and compare Omics data in plants: a case study in the crop species, Maize
journal, September 2009


Reversed-phase chromatography with multiple fraction concatenation strategy for proteome profiling of human MCF10A cells
journal, April 2011


Climate Change Impacts on Global Food Security
journal, August 2013


Stress-induced changes in the Arabidopsis thaliana transcriptome analyzed using whole-genome tiling arrays
journal, June 2009


Predicting gene regulatory networks of soybean nodulation from RNA-Seq transcriptome data
journal, January 2013


Reconstructing differentially co-expressed gene modules and regulatory networks of soybean cells
journal, January 2012


    Works referencing / citing this record: