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Proteomes 2018, 6(2), 15; https://doi.org/10.3390/proteomes6020015

Association of Proteomics Changes with Al-Sensitive Root Zones in Switchgrass

1
Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, 3500 John Merritt Blvd, Nashville, TN 37209, USA
2
R.W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY 14853, USA
*
Authors to whom correspondence should be addressed.
Received: 20 November 2017 / Revised: 13 March 2018 / Accepted: 21 March 2018 / Published: 22 March 2018
(This article belongs to the Special Issue Plant Proteomics 2017)
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Abstract

In this paper, we report on aluminum (Al)-induced root proteomic changes in switchgrass. After growth in a hydroponic culture system supplemented with 400 μM of Al, plants began to show signs of physiological stress such as a reduction in photosynthetic rate. At this time, the basal 2-cm long root tips were harvested and divided into two segments, each of 1-cm in length, for protein extraction. Al-induced changes in proteomes were identified using tandem mass tags mass spectrometry (TMT-MS)-based quantitative proteomics analysis. A total of 216 proteins (approximately 3.6% of total proteins) showed significant differences between non-Al treated control and treated groups with significant fold change (twice the standard deviation; FDR adjusted p-value < 0.05). The apical root tip tissues expressed more dramatic proteome changes (164 significantly changed proteins; 3.9% of total proteins quantified) compared to the elongation/maturation zones (52 significantly changed proteins, 1.1% of total proteins quantified). Significantly changed proteins from the apical 1-cm root apex tissues were clustered into 25 biological pathways; proteins involved in the cell cycle (rotamase FKBP 1 isoforms, and CDC48 protein) were all at a reduced abundance level compared to the non-treated control group. In the root elongation/maturation zone tissues, the identified proteins were placed into 18 pathways, among which proteins involved in secondary metabolism (lignin biosynthesis) were identified. Several STRING protein interaction networks were developed for these Al-induced significantly changed proteins. This study has identified a large number of Al-responsive proteins, including transcription factors, which will be used for exploring new Al tolerance genes and mechanisms. Data are available via ProteomeXchange with identifiers PXD008882 and PXD009125. View Full-Text
Keywords: TMT-quantitative proteomics; chromatin remodeling; genome expression reprogramming; protein sumoylation; protein folding; transcription factors; selective gene transcription and translation; physiological stress TMT-quantitative proteomics; chromatin remodeling; genome expression reprogramming; protein sumoylation; protein folding; transcription factors; selective gene transcription and translation; physiological stress
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).
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Rangu, M.; Ye, Z.; Bhatti, S.; Zhou, S.; Yang, Y.; Fish, T.; Thannhauser, T.W. Association of Proteomics Changes with Al-Sensitive Root Zones in Switchgrass. Proteomes 2018, 6, 15.

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