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

ABSTRACT: 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.

INSTRUMENT(S): LTQ Orbitrap

ORGANISM(S): Solanum Lycopersicum

TISSUE(S): Plant Cell, Root

SUBMITTER: Ted Thannhauser

LAB HEAD: Theodore Thannhauser

PROVIDER: PXD018234 | Pride | 2022-02-14

REPOSITORIES: Pride

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Using single cell type proteomics to identify Al-induced proteomes in outer layer cells and interior tissues in the apical meristem/cell division regions of tomato root-tips.

Potts Jesse J Li Hui H Qin YaoGuo Y Wu Xingbo X Hui Dafeng D Nasr Kamal Al KA Zhou Suping S Yong Yang Y Fish Tara T Liu Jiping J Thannhauser Theodore W TW

Journal of proteomics 20220120

Aluminum (Al) toxicity primarily targets the root tips, inhibiting root growth and function and leading to crop yield losses on acidic soils. Previously we reported using laser capture microdissection (LCM) proteomics to identify Al-induced proteins in the outer layer cells in the transitional zone of tomato root-tips. This study aims to further characterize Al-induced proteomic dynamics from the outer to interior tissues, thus providing a panoramic view reflecting Al resistance in the root tip ...[more]

PMID: 35066208

Similar Datasets

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

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

Project description: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.

2019-11-07 | PXD010459 | 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

Transcriptome analysis of rice roots and tips in early development by massive parallel sequencing

Project description:Despite the major physiological dissimilarities between roots and their tips, differences in their gene expression profiles remain largely unexplored. In this research, the transcriptome of rice (Oryza sativa L. subsp. Japonica) mature root tissue and root tips was monitored using mRNA-Seq at 2 time points. Almost 50 million 76 bp reads were mapped onto the rice genome sequence, differential expression patterns between tissues and time points were investigated and at least 1,006 novel transcriptionally active regions (nTARs) were detected to be expressed in rice root tissue. More than 30,000 genes were found to be expressed in rice roots, among which 1,761 root-specific and 306 tip-specific transcripts. Mature root tissue appears to respond more strongly to external stimuli than tips, showing a higher expression of for instance auxin responsive and ABA-responsive genes, as well as the phenylpropanoid pathway and photosynthesis upon light. The root tip-specific transcripts are mainly involved in mitochondrial electron transport, organelle development, secondary metabolism, DNA replication and metabolism, translation, and cellular component organization. As roots developed, genes involved in electron transport, response to oxidative stress, protein phosphorylation and metabolic processes were activated. For some nTARs a potential role in root development can be put forward based on homology to genes involved in CLAVATA signaling, cell cycle regulators and hormone signaling. A subset of differentially expressed genes and novel transcripts was confirmed using (q)RT-PCR. These results uncover previously unrecognized tissue-specific expression profiles and provide an interesting starting point to study the different regulation of transcribed regions of these tissues. 2 biological replicates of roots and 3 biological replicates of root tips were sampled at two time points (1 biological replicate contains pooled tissue from 6 plants)

2012-01-12 | E-GEOD-30367 | biostudies-arrayexpress

Laser capture microdissection and microarray analysis of ectomycorrhizas formed by the ascomycete Tuber melanosporum reveal functional heterogeneity between mantle and Hartig net compartments

Project description:The aim of this analysis was to better understand the complex symbiotic stage of Tuber melanosporum by combining the use of laser capture microdissection and microarray gene expression analysis. We isolated the fungal/soil (i.e. the mantle) and the fungal/plant (i.e. the Hartig net) interfaces from transverse sections of T. melanosporum/Corylus avellana ectomycorrhizas and identified the transcriptional landscape associated with each compartment. We compared these data to the transcriptome of ectomycorrhizal root tips, free-living mycelium and fruiting bodies of Tuber melanosporum (Series GSE17529). The T. melanosporum custom-exon expression array (4 x 72K) manufactured by Roche NimbleGen Systems Limited (Madison, WI) contained five independent, nonidentical, 60-mer probes per gene model coding sequence. Included in the oligoarray were 12,232 annotated gene models, 3,913 random 60-mer control probes and labelling controls. Sequences used for the oligonucleotide design were from an early draft of the gene catalog containing several TE families. For 1,876 gene models, technical duplicates were included on the array. We performed 6 hybridizations (NimbleGen) with samples derived from microdissected mantles (3 biological replicates) and Hartig nets ((3 biological replicates each) from T. melanosporum/Corylus avellana ectomycorrhizal root tips . All samples were labeled with Cy3.

2013-03-01 | E-GEOD-36870 | biostudies-arrayexpress

Gene expression changes in greenhouse Hebeloma cylindrosporum-Pinus pinaster ectomycorrhizal root tips compared to Hebeloma cylindrosporum free-living mycelium

Project description:Illumina HiSeq technology was used to generate mRNA profiles from Hebeloma cylindrosporum ectomycorrhizal root tips compared to free-living mycelium . Ectomycorrhizal root tips were harvested after 6 months and used for RNA extraction. Reads of 100 bp were generated and aligned to Hebeloma cylindrosporum transcripts (http://genome.jgi-psf.org/Hebcy2) using CLC Genomics Workbench 6. mRNA profiles from Hebeloma cylindrosporum ectomycorrhizal root tips and free-living mycelium were generated by Illumina HiSeq2000 sequencing (100bp). Ttwo biological replicates were sequenced for mycorrhizal and mycelium samples.

2015-07-01 | E-GEOD-66156 | biostudies-arrayexpress

Cellular and gene expression patterns associated with root bifurcation in Selaginella

Project description:To identify possible molecular mechanisms with a role in root branching initiation in S. moellendorffii, we employed the developmental root branching assay for an RNA-seq experiment and sampled root tips on each day from 0 to 5 d after the first branching (time point 0), in which 300 µm apical parts were sampled to enrich for the meristematic region, while non-meristematic root regions were sampled separately

2022-02-12 | E-MTAB-11402 | biostudies-arrayexpress

Gene expression changes in Amanita muscaria- Populus tremula x tremuloides ectomycorrhizal root tips compared to Amanita muscaria free-living mycelium

Project description:Illumina HiSeq technology was used to generate mRNA profiles from Amanita muscaria ectomycorrhizal root tips compared to free-living mycelium . Ectomycorrhizal root tips and control mycelium were harvested after 6 weeks and used for RNA extraction. Reads of 150 bp were generated and aligned to Amanita muscaria transcripts (http://genome.jgi-psf.org/Amamu1) using CLC Genomics Workbench 7. mRNA profiles from Amanita muscaria ectomycorrhizal root tips and free-living mycelium were generated by Illumina HiSeq2000 sequencing (150bp). Two biological replicates were sequenced for mycorrhizal and mycelium samples.

2015-02-06 | E-GEOD-63867 | biostudies-arrayexpress

High-througput sequencing of the rtel1 mutant

Project description:RNA sequencing performed on the root tips of rtel1 mutants and Col-0

2016-09-01 | E-MTAB-2943 | biostudies-arrayexpress