Laser microdissection: a sample preparation technique for plant micrometabolic profiling

Cell-type-specific metabolism in plants

Every plant organ contains tens of different cell types, each with a specialized function. These functions are intrinsically associated with specific metabolic flux distributions that permit the synthesis of the ATP, reducing equivalents and biosynthetic precursors demanded by the cell. Investigating such cell-type-specific metabolism is complicated by the mosaic of different cells within each tissue combined with the relative scarcity of certain types. However, techniques for the isolation of specific cells, their analysis in situ by microscopy, or modeling of their function in silico have permitted insight into cell-type-specific metabolism. In this review we present some of the methods used in the analysis of cell-type-specific metabolism before describing what we know about metabolism in several cell types that have been studied in depth; (i) leaf source and sink cells; (ii) glandular trichomes that are capable of rapid synthesis of specialized metabolites; (iii) guard cells that must accumulate large quantities of the osmolytes needed for stomatal opening; (iv) cells of seeds involved in storage of reserves; and (v) the mesophyll and bundle sheath cells of C4 plants that participate in a CO₂ concentrating cycle. Metabolism is discussed in terms of its principal features, connection to cell function and what factors affect the flux distribution. Demand for precursors and energy, availability of substrates and suppression of deleterious processes are identified as key factors in shaping cell-type-specific metabolism.

A high-efficiency trichome collection system by laser capture microdissection

Trichomes, which are classified as glandular or non-glandular, are hair-like epidermal structures that are present on aerial parts of most plant species. Glandular secretory trichomes (GSTs) have the capacity to secrete and store specialized metabolites, which are widely used as natural pesticides, food additives, fragrance ingredients or pharmaceuticals. Isolating individual trichomes is an essential way for identifying trichome-specific gene functions and discovering novel metabolites. However, the isolation of trichomes is difficult and time-consuming. Here, we report a method to isolate the GSTs from leaf epidermis dispense with fixation using laser capture microdissection (LCM). In this study, 150 GSTs were captured efficiently from Artemisia annua leaves and enriched for artemisinin measurement. UPLC analysis of microdissected samples indicated specific accumulation of secondary metabolites could be detected from a small number of GSTs. In addition, qRT-PCR revealed that the GST-specific structural genes involved in artemisinin biosynthesis pathway were highly expressed in GSTs. Taken together, we developed an efficient method to collect comparatively pure GSTs from unfixed leaved, so that the metabolites were relatively obtained intact. This method can be implemented in metabolomics research of purely specific plant cell populations and has the potential to discover novel secondary metabolites.

Spatially resolved absolute quantitation in thin tissue by mass spectrometry

Mass spectrometry (MS) has become the de facto tool for routine quantitative analysis of biomolecules. MS is increasingly being used to reveal the spatial distribution of proteins, metabolites, and pharmaceuticals in tissue and interest in this area has led to a number of novel spatially resolved MS technologies. Most spatially resolved MS measurements are qualitative in nature due to a myriad of potential biases, such as sample heterogeneity, sampling artifacts, and ionization effects. As applications of spatially resolved MS in the pharmacological and clinical fields increase, demand has become high for quantitative MS imaging and profiling data. As a result, several varied technologies now exist that provide differing levels of spatial and quantitative information. This review provides an overview of MS profiling and imaging technologies that have demonstrated quantitative analysis from tissue. Focus is given on the fundamental processes affecting quantitative analysis in an array of MS imaging and profiling technologies and methods to address these biases.Graphical abstract.

Laser-assisted optoporation of cells and tissues - a mini-review

Laser microbeam techniques are presented, which permit the introduction of molecules or small particles into living cells. Possible mechanisms - including photochemical, photothermal and opto-mechanical interactions (ablations) - are induced by continuous wave (cw) or pulsed lasers of different wavelength, power, and mode of operation. Laser-assisted optoporation permits the uptake of fluorescent dyes as well as DNA plasmids for cell transfection, and, in addition to its broad application to cultivated cells, may have some clinical potential.

Strategy for the analysis of tissue-specific methylation changes without physical isolation

One common experimental hurdle that arises when explore patterns of cytosine methylation is the generation of data derived from a single specific tissue, often arduous to isolate from a heterogeneous biospecimen. Here we show a new strategy for exploring environment- or mutation-caused changes in cell type- or tissue-specific methylation landscapes, which requires neither transgenic reporter cell lines nor physical separation. This approach takes advantage of a known distinct methylation signature existing in only one of the tissues within an organ under a particular condition. From the information on such compared published methylomes, one can design a set of PCR primers that specifically amplify bisulfite-converted DNA of two nearby genomic regions of interest, thus allowing for tissue-specific DNA methylation data. To validate the performance of the approach, we designed primers able to amplify a portion of a gene in the context of root biology: the Arabidopsis homeotic gene Glabra-2 (Gl2), expressed only in epidermis during cell differentiation. We found that the extent of methylated cytosines appears remarkably different when root epidermis-specific primers were used vs. non-specific ones under three genetic backgrounds involving mutations in genes also associated with the establishment of cell identity. Although the genetic or environmental perturbations to be studied might modify methylation in the primer-annealing zone, leading to a possible misinterpretation of the data, the strategy presented here can become a useful first round screening tool to detect differences in tissue-specific epigenetic status under new conditions.

Localisation of Two Bioactive Labdane Diterpenoids in the Peltate Glandular Trichomes of Leonurus japonicus by Laser Microdissection Coupled with UPLC-MS/MS

INTRODUCTION

Glandular trichomes of plants are biochemical factories that could produce, store and secrete copious pharmaceutically important natural products. The Labiatae plant Leonurus japonicus is an important traditional Chinese medicine used to treat gynecological diseases, and has abundant peltate glandular trichomes (PGTs), in which the secondary metabolites accumulated are still unknown.

OBJECTIVE

To study the secondary metabolites specifically accumulated in the PGTs of L. japonicus and their biological activities, and provide a new way to pinpoint bioactive natural products from plants.

METHODOLOGY

Morphology of the trichomes on L. japonicus were observed under a scanning electron microscope. The PGTs of L. japonicus were precisely collected using laser microdissection (LMD) and analysed for their secondary metabolites with ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). Targeted compounds were isolated with classical phytochemical methods, and their structures were elucidated by spectroscopic analysis. Biological activities were evaluated by in vitro assays.

RESULTS

Two labdane diterpenoids, leoheterin (1) and galeopsin (2), were localised in the PGTs of L. japonicus. Antithrombotic activity of 1 in anti-platelet aggregation assay induced by arachidonic acid was observed. Both compounds showed potential anti-inflammatory activity by inhibiting proinflammatory cytokine TNF-α. In addition, anti-proliferative effect of both compounds on several cancer cell lines was also detected.

CONCLUSION

Two bioactive labdane diterpenoids were localised in the PGTs of L. japonicus. The findings suggested that it might be an efficient approach to explore bioactive natural products from the glandular trichomes of medicinal plants with LMD-UPLC/MS/MS. Copyright © 2017 John Wiley & Sons, Ltd.

Laser microdissection: A promising tool for exploring microorganisms and their interactions with hosts

Laser microdissection is a method that allows for the isolation of homogenous cell populations from their native niches in tissues for downstream molecular assays. This method is widely used for genomic analysis, gene expression profiling and proteomic and metabolite assays in various fields of biology, but it remains an uncommon approach in microbiological research. In spite of the limited number of publications, laser microdissection was shown to be an extremely useful method for studying host-microorganism interactions in animals and plants, investigating bacteria within biofilms, identifying uncultivated bacteria and performing single prokaryotic cell analysis. The current paper describes the methodological aspects of commercially available laser microdissection instruments and representative examples that demonstrate the advantages of this method for resolving a variety of issues in microbiology.

Tissue-specific metabolite profiling of benzylisoquinoline alkaloids in the root of Macleaya cordata by combining laser microdissection with ultra-high-performance liquid chromatography/tandem mass spectrometry

RATIONALE

Tissue-specific metabolite profiling helps to find trace alkaloids masked during organ analysis, which contributes to understanding the alkaloid biosynthetic pathways in vivo and evaluating the quality of medical plants by morphology. As Macleaya cordata contains diverse types of benzylisoquinoline alkaloids (BIAs), the alkaloid metabolite profiling was carried out on various tissues of the root.

METHODS

Laser microdissection with fluorescence detection was used to recognize and dissect different tissues from the root of M. cordata. Ultra-high-performance liquid chromatography/quadrupole time-of-flight mass spectrometry was applied to analyze the trace alkaloids in tissues. These detected alkaloids were elucidated using their accurate molecular weights, MS/MS data, MS fragmentation patterns and the known biosynthetic pathways of BIAs. Finally, the distribution of alkaloids in dissected tissues and whole sections was mapped.

RESULTS

Forty-nine alkaloids were identified from five microdissected tissues, and 24 of them were detected for the first time in M. cordata. Some types of alkaloids occurred specifically in dissected tissues. More alkaloids were detected in the cork and xylem vascular bundles which emit strong fluorescence under fluorescence microscopy. Some of the screened alkaloids were intermediates in sanguinarine and chelerythrine biosynthetic pathways, and others were speculated to be involved in the new branches of biosynthetic pathways.

CONCLUSIONS

The integrated method is sensitive, specific and reliable for determining trace alkaloids, which is also a powerful tool for metabolite profiling of tissue-specific BIAs in situ. The present findings should contribute to a better understanding of the biosynthesis of BIAs in M. cordata root and provide scientific evidence for its quality evaluation based on morphological characteristics. Copyright © 2016 John Wiley & Sons, Ltd.

The Recent Developments in Sample Preparation for Mass Spectrometry-Based Metabolomics

Metabolomics is a critical member in systems biology. Although great progress has been achieved in metabolomics, there are still some problems in sample preparation, data processing and data interpretation. In this review, we intend to explore the roles, challenges and trends in sample preparation for mass spectrometry- (MS-) based metabolomics. The newly emerged sample preparation methods were also critically examined, including laser microdissection, in vivo sampling, dried blood spot, microwave, ultrasound and enzyme-assisted extraction, as well as microextraction techniques. Finally, we provide some conclusions and perspectives for sample preparation in MS-based metabolomics.

Laser Capture Microdissection: Avoiding Bias in Analysis by Selecting Just What Matters

Laser capture microdissection (LCM) is a powerful technique for harvesting specific cells from a heterogeneous population. As each cell and tissue has its unique genetic, proteomic, and metabolic profile, the use of homogeneous samples is important for a better understanding of complex processes in both animal and plant systems. In case of plants, LCM is very suitable as the highly regular tissue organization and stable cell walls from these organisms enable visual identification of various cell types without staining of tissue sections, which can prevent some downstream analysis. Considering the applicability of LCM to any plant species, here we provide a step-by-step protocol for selecting specific cells or tissues through this technology.

Comparative transcriptional analysis provides new insights into the molecular basis of adventitious rooting recalcitrance in Eucalyptus

Adventitious rooting (AR) is essential in clonal propagation. Eucalyptus globulus is relevant for the cellulose industry due to its low lignin content. However, several useful clones are recalcitrant to AR, often requiring exogenous auxin, adding cost to clonal garden operations. In contrast, E. grandis is an easy-to-root species widely used in clonal forestry. Aiming at contributing to the elucidation of recalcitrance causes in E. globulus, we conducted a comparative analysis with these two species differing in rooting competence, combining gene expression and anatomical techniques. Recalcitrance in E. globulus is reversed by exposure to exogenous indole-3-acetic acid (IAA), which promotes important gene expression modifications in both species. The endogenous content of IAA was significantly higher in E. grandis than in E. globulus. The cambium zone was identified as an active area during AR, concentrating the first cell divisions. Immunolocalization assay showed auxin accumulation in cambium cells, further indicating the importance of this region for rooting. We then performed a cambium zone-specific gene expression analysis during AR using laser microdissection. The results indicated that the auxin-related genes TOPLESS and IAA12/BODENLOS and the cytokinin-related gene ARR1may act as negative regulators of AR, possibly contributing to the hard-to-root phenotype of E. globulus.

Symbiosis dependent accumulation of primary metabolites in arbuscule-containing cells

BACKGROUND

The arbuscular mycorrhizal symbiosis is characterized by the presence of different symbiotic structures and stages within a root system. Therefore tools allowing the analysis of molecular changes at a cellular level are required to reveal insight into arbuscular mycorrhizal (AM) symbiosis development and functioning.

RESULTS

Here we describe the analysis of metabolite pools in arbuscule-containing cells, which are the site of nutrient transfer between AM fungus and host plant. Laser capture microdissection (LCM) combined with gas chromatography mass spectrometry (GC-EI/TOF-MS) enabled the analysis of primary metabolite levels,which might be of plant or fungal origin, within these cells.

CONCLUSIONS

High levels of the amino acids, aspartate, asparagine, glutamate, and glutamine, were observed in arbuscule-containing cells. Elevated amounts of sucrose and the steady-state of hexose levels indicated a direct assimilation of monosaccharides by the fungal partner.

Investigation of the Chemical Interface in the Soybean-Aphid and Rice-Bacteria Interactions Using MALDI-Mass Spectrometry Imaging

Mass spectrometry imaging (MSI) is an emerging technology for high-resolution plant biology. It has been utilized to study plant-pest interactions, but limited to the surface interfaces. Here we expand the technology to explore the chemical interactions occurring inside the plant tissues. Two sample preparation methods, imprinting and fracturing, were developed and applied, for the first time, to visualize internal metabolites of leaves in matrix-assisted laser desorption ionization (MALDI)-MSI. This is also the first time nanoparticle-based ionization was implemented to ionize diterpenoid phytochemicals that were difficult to analyze with traditional organic matrices. The interactions between rice-bacterium and soybean-aphid were investigated as two model systems to demonstrate the capability of high-resolution MSI based on MALDI. Localized molecular information on various plant- or pest-derived chemicals provided valuable insight for the molecular processes occurring during the plant-pest interactions. Specifically, salicylic acid and isoflavone based resistance was visualized in the soybean-aphid system and antibiotic diterpenoids in rice-bacterium interactions.

Plant single-cell and single-cell-type metabolomics

In conjunction with genomics, transcriptomics, and proteomics, plant metabolomics is providing large data sets that are paving the way towards a comprehensive and holistic understanding of plant growth, development, defense, and productivity. However, dilution effects from organ- and tissue-based sampling of metabolomes have limited our understanding of the intricate regulation of metabolic pathways and networks at the cellular level. Recent advances in metabolomics methodologies, along with the post-genomic expansion of bioinformatics knowledge and functional genomics tools, have allowed the gathering of enriched information on individual cells and single cell types. Here we review progress, current status, opportunities, and challenges presented by single cell-based metabolomics research in plants.

The dynamic behavior of storage organelles in developing cereal seeds and its impact on the production of recombinant proteins

Cereal endosperm is a highly differentiated tissue containing specialized organelles for the accumulation of storage proteins, which are ultimately deposited either within protein bodies derived from the endoplasmic reticulum, or in protein storage vacuoles (PSVs). During seed maturation endosperm cells undergo a rapid sequence of developmental changes, including extensive reorganization and rearrangement of the endomembrane system and protein transport via several developmentally regulated trafficking routes. Storage organelles have been characterized in great detail by the histochemical analysis of fixed immature tissue samples. More recently, in vivo imaging and the use of tonoplast markers and fluorescent organelle tracers have provided further insight into the dynamic morphology of PSVs in different cell layers of the developing endosperm. This is relevant for biotechnological applications in the area of molecular farming because seed storage organelles in different cereal crops offer alternative subcellular destinations for the deposition of recombinant proteins that can reduce proteolytic degradation, allow control over glycan structures and increase the efficacy of oral delivery. We discuss how the specialized architecture and developmental changes of the endomembrane system in endosperm cells may influence the subcellular fate and post-translational modification of recombinant glycoproteins in different cereal species.