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 »
- Authors:
-
- 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
- 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 Iztacalav
- Univ. of Missouri, Columbia, MO (United States). C.S. Bond Life Sciences Center, Informatics Inst.
- 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
- 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
- Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Environmental Molecular Sciences Lab. (EMSL)
- Publication Date:
- Research Org.:
- Pacific Northwest National Laboratory (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. https://doi.org/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. https://doi.org/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 = {Mon Apr 25 00:00:00 EDT 2016},
month = {Mon Apr 25 00:00:00 EDT 2016}
}
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Sex-specific and lineage-specific alternative splicing in primates
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Establishment of a Protein Reference Map for Soybean Root Hair Cells
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Complete Transcriptome of the Soybean Root Hair Cell, a Single-Cell Model, and Its Alteration in Response to Bradyrhizobium japonicum Infection
journal, November 2009
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A guide to using MapMan to visualize and compare Omics data in plants: a case study in the crop species, Maize
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Heat stress induction of miR398 triggers a regulatory loop that is critical for thermotolerance in Arabidopsis
journal, April 2013
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Correlation of mRNA and protein abundance in the developing maize leaf
journal, April 2014
- Ponnala, Lalit; Wang, Yupeng; Sun, Qi
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Climate Change Impacts on Global Food Security
journal, August 2013
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Predicting gene regulatory networks of soybean nodulation from RNA-Seq transcriptome data
journal, January 2013
- Zhu, Mingzhu; Dahmen, Jeremy L.; Stacey, Gary
- BMC Bioinformatics, Vol. 14, Issue 1
Soybean Knowledge Base (SoyKB): a web resource for soybean translational genomics
journal, January 2012
- Joshi, Trupti; Patil, Kapil; Fitzpatrick, Michael R.
- BMC Genomics, Vol. 13, Issue Suppl 1
Transcriptomic analysis of Sorghum bicolor responding to combined heat and drought stress
journal, January 2014
- Johnson, Stephanie M.; Lim, Fei-Ling; Finkler, Aliza
- BMC Genomics, Vol. 15, Issue 1
Transcriptome analysis of heat stress response in switchgrass (Panicum virgatum L.)
journal, January 2013
- Li, Yong-Fang; Wang, Yixing; Tang, Yuhong
- BMC Plant Biology, Vol. 13, Issue 1
Differential proteomic analysis of grapevine leaves by iTRAQ reveals responses to heat stress and subsequent recovery
journal, January 2014
- Liu, Guo-Tian; Ma, Ling; Duan, Wei
- BMC Plant Biology, Vol. 14, Issue 1
In Silico Estimation of Translation Efficiency in Human Cell Lines: Potential Evidence for Widespread Translational Control
journal, February 2013
- Stevens, Stewart G.; Brown, Chris M.
- PLoS ONE, Vol. 8, Issue 2
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
Genome scale transcriptional response diversity among ten ecotypes of Arabidopsis thaliana during heat stress
journal, January 2013
- Barah, Pankaj; Jayavelu, Naresh D.; Mundy, John
- Frontiers in Plant Science, Vol. 4
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
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
Temperature-regulation of plant architecture
journal, July 2009
- Patel, Dhaval; Franklin, Keara A.
- Plant Signaling & Behavior, Vol. 4, Issue 7
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