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LCM-quantitative proteomics analysis of Al-sensitive tomato root cells

ABSTRACT: Aluminum toxicity in acid soil is a major stress to plant growth. The primary target is in root-tips where the epidermal and outer cortex layers of cells in the root transition zone area are more sensitive to the toxic ions. This project used laser capture microdissection (LCM) technology to isolate these Al-sensitive cells. Tandem mass tag (TMT) proteomics was used to identify Al- induced proteomes. The information was used to determine functions of protein changes in response to Al toxicity in these Al-sensitive root cells.

INSTRUMENT(S): LTQ Orbitrap

ORGANISM(S): Bemisia Sp. Unknown_th_13_12_s.lycopersicum

TISSUE(S): Plant Cell, Root

SUBMITTER: Ted Thannhauser

LAB HEAD: Theodore W. Thannhauser

PROVIDER: PXD010459 | Pride | 2019-11-07

REPOSITORIES: Pride

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			Action	DRS
	19Jan2018_Suping_LCM_TomatoRoot.msf	Msf
	19Jan2018_Suping_LCM_TomatoRoot.mzML	Mzml
	19Jan2018_Suping_LCM_TomatoRoot.mzid	Mzid
	20Jan2018_Suping_LCM_TomatoRoot_F1.raw	Raw
	20Jan2018_Suping_LCM_TomatoRoot_F2.raw	Raw

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Publications

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

Yang Shaolan S Li Hui H Bhatti Sarabjit S Zhou Suping S Yang Yong Y Fish Tara T Thannhauser Theodore W TW

Journal of proteomics 20191024

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 Al<sup>3+</sup> 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 ...[more]

PMID: 31669359

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Al-induced root proteomics changes in stress-acclimated tomato plants

Project description:Excess levels of Al3+ become highly harmful to plant roots as the toxic ions bind to the surface of root-tips. Plants can acquire tolerance to stress after multiple generations of exposure to stress conditions. After four consecutive generations of Al treatments (G4Al+ seeds), tomato plants appeared more tolerant to the stress condition. This project used laser capture microdissection (LCM) technology to isolate the Al-sensitive epidermal and outer cortical cells of root-tips. Tandem mass tag (TMT) proteomics analysis was conducted to identify proteomics changes related to the physiological properties in root growth under Al treated conditions.

2022-02-14 | PXD018234 | Pride

Proteomics studies of outer and inner cellular layers of tomato root-tips for Al stress

Project description:Excess levels of Al3+ become highly harmful to plant roots. The epidermal and outer cortical layers of root-tips experience more severe damages than the inner tissues from Al toxicity. This project used laser capture microdissection (LCM) technology to isolate the outer and inner cell layers of cells in root-tips. Tomato "MicroTom" plants were grown in hydroponic solution supplemented with Al. Seeds derived from plants previously exposed to four generations of Al-treated solutions were considered stress-acclimated, these seeds were named G4Al+. Seeds harvested from soil-grown plants were also used, these seeds were named G0 seeds. Tandem mass tag (TMT) proteomics was used to identify differential proteomics responses among cells localized at different spaces in root-tips and those between the stress-acclimated and non-acclimated plants.

2022-02-14 | PXD021994 | Pride

Heat-induced proteomes in tomato pollen mother cells

Project description:Tomato pollen production and viability is highly vulnerable to higher temperature. Hot summers with temperature reaching above 32°C can disrupt production of viable pollens and fruit set, resulting in yield loss. In recent years, temperature above 35-38oC has become a norm during mid-summer with potential adverse impacts on the production of tomatoes and many other crop species. Pollens are developed through the microsporogenesis and micro-gametogenesis stages. The most heat sensitive period is from the meiotic process of the microsporocytes, at the young microspore stage (uninucleate stage of microspore) to during late pollen development (pollen mitosis). This project studied the heat-induced proteomes in microsporocyte, also called pollen mother cells (PMC). Homogenous PMC samples were collected from cross-sectioned frozen fresh anther tissues of tomato ‘Maxifort’ using laser capture microdissection (LCM). Tandem mass tag (TMT) proteomics analysis was conducted to identify proteomics changes related to heat tolerance during pollen development.

2022-04-07 | PXD018915 | Pride

Association of proteomics changes with Al-sensitive root zones in switchgrass

Project description:In this project, we report on aluminum (Al)-induced root proteomic changes in switchgrass. After growth in a hydroponic culture system supplemented with 400μM 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, q<0.05). The basal 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 basal-1cm root apex tissues were clustered into 25 biological pathways, three proteins in cell cycles were all at a reduced abundance level compared to the non-treated control group. In the root elongation and maturation zone tissues, the identified proteins were placed into 18 pathways, proteins in secondary cell wall formation (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.

2018-03-23 | PXD008882 | Pride

Association of proteomics changes with Al-sensitive root zones in switchgrass, part 2

2018-03-19 | PXD009125 | Pride

19Jan2018_Suping_LCM_TomatoHeatPollen_protein only

Project description:Heat stress is a major challenge for crop production. During the reproduction stage, pollen development is the most sensitive process to abnormal environmental conditions. In this project, we have developed a heat treatment system for tomato where plants produce a significantly lower number of pollens and the germination rate of those pollens was also very low. The size of the flower buds and pollen developmental stages were examined under confocal microscope. Pollen cells at different developmental stages were collected from flower buds at corresponding sizes using LCM. The single cell population proteomics analysis was used to identify proteome changes in a distinct group of cells. This information was used to determine the function of proteins that are associated with heat stress on cellular processes/functions during pollen development.

2022-02-23 | PXD010218 | Pride

Agilent 44K Rice Oligo DNA Microarray RAP-DB (G2519F#15241); genome-wide transcriptional analysis of Aluminum-responsive genes in rice (Oryza sativa).

Project description:By comparing transcriptional profiling between a wild-type rice and an Al-sensitive rice mutant star1, we found that rice possesses novel mechanisms of Al-tolerance in addition to ART1-regulated mechanism in rice. The transcriptional profiling between the wild-type rice and an Al-sensitive mutant, star1. +Al vs. -Al in the roots of wild-type rice and star1 mutant. Biological replicates: +Al/-Al WT root tip 4 replicates, +Al/-Al WT basal tip 4 replicates, +Al/-Al star1 root tip 4 replicates, +Al/-Al star1 basal tip 4 replicates

2012-09-19 | E-GEOD-40964 | biostudies-arrayexpress

Lateral root meristem establishment by LRIS in Arabidopsis

Project description:Previous transcript profiling of the Arabidopsis LRIS only occurred after 2 and 6 hours of NAA treatment (Himanen et al., 2004, Vanneste et al., 2005, De Smet et al., 2008). Here, we extended the time-course of the Arabidopsis LRIS to capture the expression during primordium formation. Therefore, we first characterized lateral root primordium development in the Arabidopsis LRIS, and performed staging in different regions of the root. We observed a slight loss of the synchronization in higher parts of the root. Nevertheless at 1 to 2 mm distance from the root tip, different stages of primordia were highly synchronously induced, and stage I, II and III primordia could be observed at 12, 18 and 24 hours after NAA treatment, respectively. We therefore sampled the 1 to 2 mm region from the root tip at 0, 12, 18 and 24 hours in the Arabidopsis LRIS, to sample stage I, II and III primordia, respectively.

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Transcriptomics analysis of Prunus L: Differential adaptative responses during short and long term hypoxia treatment

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2016-12-09 | E-MTAB-4213 | biostudies-arrayexpress

Aluminum and salt induced protein changes in tomato plants transformed with bar gene

Project description:In this project, seedlings of tomato (Solanum lycopersicum) ‘Money Maker’ plants transformed with a bar gene were treated under 20 µM Al3+ and salt (200 mM NaCl) for two weeks. The treatments were conducted in hydroponic solutions in a greenhouse at 24±2C without supplemental light. Roots harvested were immediately frozen in liquid nitrogen and stored at -80 oC. The treatment experiment was conducted at Agricultural Research Station, Tennessee State University, Nashville, TN 37209

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