The Al-induced proteomes of epidermal and outer cortical cells in root apex of cherry tomato 'LA 2710'

Shaolan Yang; Hui Li; Sarabjit Bhatti; Suping Zhou; Yong Yang; Tara Fish; Theodore W Thannhauser

doi:10.1016/j.jprot.2019.103560

The Al-induced proteomes of epidermal and outer cortical cells in root apex of cherry tomato 'LA 2710'

J Proteomics. 2020 Jan 16:211:103560. doi: 10.1016/j.jprot.2019.103560. Epub 2019 Oct 24.

Authors

Shaolan Yang¹, Hui Li², Sarabjit Bhatti², Suping Zhou³, Yong Yang⁴, Tara Fish⁴, Theodore W Thannhauser⁵

Affiliations

¹ Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, 3500 John Merritt Blvd, Nashville, TN 37209, USA; College of Horticulture, Qingdao Agricultural University, Qingdao, Shandong 266109, China.
² Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, 3500 John Merritt Blvd, Nashville, TN 37209, USA.
³ Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, 3500 John Merritt Blvd, Nashville, TN 37209, USA. Electronic address: zsuping@tnstate.edu.
⁴ R.W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY 14853, USA.
⁵ R.W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY 14853, USA. Electronic address: tt34@cornell.edu.

PMID: 31669359
DOI: 10.1016/j.jprot.2019.103560

Abstract

This paper reports a laser capture microdissection-tandem mass tag-quantitative proteomics analysis of Al-sensitive cells in root tips. Cherry tomato (Solanum lycopersicum var. cerasiforme 'LA2710') seedlings were treated under 15 μM Al³⁺ activity for 13 d. Root-tip longitudinal fresh frozen tissue sections of 10 μm thickness were prepared. The Al-sensitive root zone and cells were determined using histochemical analysis of root-tips and micro-sections. A procedure for collecting the Al-sensitive cells using laser capture microdissection-protein extraction-tandem mass tag-proteomics analysis was developed. Proteomics analysis of 18 μg protein/sample with three biological replicates per treatment condition identified 3879 quantifiable proteins each associated with two or more unique peptides. Quantified proteins constituted a broad range of Kyoto Encyclopedia of Genes and Genomes pathways when searched in the annotated tomato genome. Differentially expressed proteins between the Al-treated and non-Al treated control conditions were identified, including 128 Al-up-regulated and 32 Al-down-regulated proteins. Analysis of functional pathways and protein-protein interaction networks showed that the Al-down-regulated proteins are involved in transcription and translation, and the Al-up-regulated proteins are associated with antioxidant and detoxification and protein quality control processes. The proteomics data are available via ProteomeXchange with identifier PXD010459 under project title 'LCM-quantitative proteomics analysis of Al-sensitive tomato root cells'. SIGNIFICANCE: This paper presents an efficient laser capture microdissection-tandem mass tag-quantitative proteomics analysis platform for the analysis of Al sensitive root cells. The analytical procedure has a broad application for proteomics analysis of spatially separated cells from complex tissues. This study has provided a comprehensive proteomics dataset expressed in the epidermal and outer-cortical cells at root-tip transition zone of Al-treated tomato seedlings. The proteomes from the Al-sensitive root cells are valuable resources for understanding and improving Al tolerance in plants.

Keywords: Al stress; Laser capture microdissection-tandem mass tag-proteomics; Protein functional classification; Protein-protein interaction network; Single cell type root-tip proteomics; Tomato.

Published by Elsevier B.V.

Publication types

Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Laser Capture Microdissection
Proteome*
Proteomics
Seedlings
Solanum lycopersicum*

Substances

Proteome