Single-Cell Metabolite Profiling of Stalk and Glandular Cells of Intact Trichomes with Internal Electrode Capillary Pressure Probe Electrospray Ionization Mass Spectrometry

Nakashima, Taiken; Wada, Hiroshi; Morita, Satoshi; Erra‐Balsells, Rosa; Hiraoka, Kenzo; Nonami, Hiroshi

doi:10.1021/acs.analchem.5b03366

Cited by 86 publications

(75 citation statements)

References 48 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…For example, some plant specialized metabolites such as glucosinolates and terpenoids confer resistance against insects and pathogens (6,10). Another difference between general and specialized metabolites is that the later tend to accumulate in specific tissues such as in trichomes or fruit (11,12). In addition to their ecological and evolutionary importance, specialized metabolites are important for human health; ~25% of medicinal compounds are derived from plant metabolites (5,13).…”

Section: /Bodymentioning

confidence: 99%

Within and cross species predictions of plant specialized metabolism genes using transfer learning

Moore

Wang

Fan

et al. 2020

Preprint

View full text Add to dashboard Cite

Plant specialized metabolites mediate interactions between plants and the environment and have significant agronomical/pharmaceutical value. Most genes involved in specialized metabolism (SM) are unknown because of the large number of specialized metabolites and the challenge in differentiating SM genes from general metabolism (GM) genes. We employed transfer learning, a machine learning strategy in which information from one species with substantially more experimentally derived function data (Arabidopsis thaliana) is used to build a model to predict gene functions in another species (Solanum lycopersicum). Using machine learning to integrate heterogenous gene features, we built models distinguishing tomato SM and GM genes. Although SM/GM genes can be predicted based on tomato data alone (F-measure=0.74, compared with 0.5 for random and 1.0 for perfect predictions), using information from Arabidopsis to filter likely misannotated genes significantly improves prediction (F-measure= 0.92). This study demonstrates that SM/GM genes can be better predicted by leveraging cross-species information. SignificanceWith the increase of sequenced non-model species, a major challenge in plant biology is to ascertain gene function. Model species such as Arabidopsis thaliana have large amounts of experimentally-backed annotations that non-model species lack. We show how to use a model species to better annotate the function of genes in a non-model species using a technique called transfer learning. In particular, we focus on genes involved in specialized metabolism (SM), or metabolism specific to a certain plant lineage, which are not well known because of the sizeable diversity of specialized metabolites (SMs) among plant species. We use Arabidopsis to predict SM genes in tomato, a species with many SMs of interest but with a poorer annotation than Arabidopsis.

show abstract

Section: /Bodymentioning

confidence: 99%

Within and cross species predictions of plant specialized metabolism genes using transfer learning

Moore

Wang

Fan

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“…148 In a PESI-inspired approach, Nakashima et al developed a pressure PESI-MS with internal electrode capillary (IEC-PPESI-MS) which enabled high spatial-resolution cell sampling, precise post-sampling manipulation, and high detection sensitivity for in situ single-cell metabolite profiling. 149 The capability of the technique was evaluated with the analysis of amino acids, organic acids, carbohydrates, and flavonoid in stalk and glandular cells that form a trichome unit in tomato plants ( Solanum lycopersicum L . ), showing metabolic differentiation between two cell types as well as among different types of trichomes.…”

Section: Plant Biology and Agriculturementioning

confidence: 99%

“…), showing metabolic differentiation between two cell types as well as among different types of trichomes. 149 Etalo et al performed a series of experiments on plant tissues to highlight the usefulness as well as the challenges of using LAESI-MSI for in situ metabolomic analysis. 150 The water content dependence was seen to affect the material ablation process and to be critical for efficient ionization.…”

Section: Plant Biology and Agriculturementioning

confidence: 99%

Ambient mass spectrometry in metabolomics

Clendinen

Monge

Fernández

2017

Analyst

View full text Add to dashboard Cite

Since the introduction of desorption electrospray ionization (DESI) mass spectrometry (MS), ambient MS methods have seen increased use in a variety of fields from health to food science. Increasing its popularity in metabolomics, ambient MS offers limited sample preparation, rapid and direct analysis of liquids, solids, and gases, in situ and in vivo analysis, and imaging. The metabolome consists of a constantly changing collection of small (<1.5KDa) molecules. These include endogenous molecules that are part of primary metabolism pathways, secondary metabolites with specific functions such as signaling, chemicals incorporated in the diet or resulting from environmental exposures, and metabolites associated with the microbiome. Characterization of the responsive changes of this molecule cohort is the principle goal in any metabolomics study. With adjustments to experimental parameters, metabolites across a range of chemical and physical properties can be selectively desorbed and ionized and subsequently analyzed with increased speed and sensitivity. This review covers the broad applications of a variety of ambient MS techniques in four primary fields in which metabolomics is commonly employed.

show abstract

“…This minimally invasive approach has been used to quantify cell-to-cell variation in water relations in-situ (Nonami and Schulze 1989). The CPP has also been used to collect cellular fluids for metabolite analyses in order to reveal spatial variations in cellular metabolism using enzymatic assays (Koroleva et al 1997) and more recently mass spectrometry-assisted cell metabolomics (Nakashima et al 2016; Wada et al 2019).…”

Section: Introductionmentioning

confidence: 99%

Minimally invasive, pressure probe based sampling allows for in-situ gene expression analyses in plant cells

Wada

Castellarin

Matthews

et al. 2019

Preprint

Self Cite

View full text Add to dashboard Cite

24Background: Gene expression analyses are conducted using multiple approaches and 25 increasingly research has been focused on assessing gene expression at the level of a 26 tissue or even single-cells. To date, methods to assess gene expression at the single-cell in 27 plant tissues have been semi-quantitative, require tissue disruption, and/or involve laborious, 28 possibly artifact-inducing manipulation. In this work, we used grape berries (Vitis vinifera L. 29 Zinfandel) as a model in order to examine the validity and reproducibility of an in-situ gene 30 expression analysis method combining a cell pressure probe (CPP) with quantitative PCR 31 (qPCR).32 Results: We developed a method to directly assess gene expression levels via qPCR from 33 cellular fluids sampled in-situ with a CPP. Cellular fluids, with volumes in the picoliter range, 34 were collected from intact berries with a CPP at various depths across skin and mesocarp 35 tissues. The expression of a key anthocyanin biosynthetic gene, UDP-glucose: flavonoid 3-36 O-glucosyltransferase (VviUFGT), was analyzed as a test case since its expression is 37 restricted to cells producing anthocyanins in grape berry skins during ripening. The method 38 identifies samples contaminated with significant levels of genomic DNA by amplifying a 39 region of VviUFGT that spans an intron. Therefore false positives were discarded which 40 occurred in 28% of the samples tested. Shallow probing of skin cells showed high VviUFGT 41 expression as expected while deeper probing of mesocarp cells resulted in no VviUFGT 42 expression. 43 Conclusions: The clear correspondence of VviUFGT expression to the targeted cell 44 samples suggests that the in-situ gene expression analysis using a CPP is reliable and does 45 not result in contamination as the probe moves through tissues. This method can be paired 46 to single-cell transcriptomic analyses in the future. We conclude that this technique 47 235 exons flanking the intron. The expression of VviUFGT was analysed by these primer pairs: 236 VviUFGT-forward (5'-GCAGGGCCTAACTCACTCTC-3'), VviUFGT-reverse (5'-237 AAATTGAGCAGCTCGTCTTCA-3'), and VviUbi was analyzed according to (Castellarin et 238 al. 2007a). The final PCR products obtained from the VviUFGT amplification were analyzed 239 9 in 1.5 % agarose gel. The samples that amplified two bands, 178bp (VviUFGT gDNA) and 240 101bp (VviUFGT mRNA) bands, were discarded because of the gDNA comtamination. The 241 samples with only a 101bp band were considered to be positive samples and included in the 242 data analysis. VviUFGT gene expression is reported relative to VviUbi. 243 244 Declarations 245

show abstract

Single-Cell Metabolite Profiling of Stalk and Glandular Cells of Intact Trichomes with Internal Electrode Capillary Pressure Probe Electrospray Ionization Mass Spectrometry

Cited by 86 publications

References 48 publications

Within and cross species predictions of plant specialized metabolism genes using transfer learning

Within and cross species predictions of plant specialized metabolism genes using transfer learning

Ambient mass spectrometry in metabolomics

Minimally invasive, pressure probe based sampling allows for in-situ gene expression analyses in plant cells

Contact Info

Product

Resources

About