scholarly journals Staring into the void: demystifying microbial metabolomics

2019 ◽  
Vol 366 (11) ◽  
Author(s):  
Cynthia M Grim ◽  
Gordon T Luu ◽  
Laura M Sanchez
Keyword(s):  
Mass Spectrometry ◽  
Biological Significance ◽  
Analytical Techniques ◽  
Liquid Chromatography Mass Spectrometry ◽  
Single Experiment ◽  
Primary Metabolites ◽  
Transposon Insertion ◽  
Strong Focus ◽  
Limited Mass ◽  
Informatics Tools

ABSTRACT Metabolites give us a window into the chemistry of microbes and are split into two subclasses: primary and secondary. Primary metabolites are required for life whereas secondary metabolites have historically been classified as those appearing after exponential growth and are not necessarily needed for survival. Many microbial species are estimated to produce hundreds of metabolites and can be affected by differing nutrients. Using various analytical techniques, metabolites can be directly detected in order to elucidate their biological significance. Currently, a single experiment can produce anywhere from megabytes to terabytes of data. This big data has motivated scientists to develop informatics tools to help target specific metabolites or sets of metabolites. Broadly, it is imperative to identify clear biological questions before embarking on a study of metabolites (metabolomics). For instance, studying the effect of a transposon insertion on phenazine biosynthesis in Pseudomonas is a very different from asking what molecules are present in a specific banana-derived strain of Pseudomonas. This review is meant to serve as a primer for a ‘choose your own adventure’ approach for microbiologists with limited mass spectrometry expertise, with a strong focus on liquid chromatography mass spectrometry based workflows developed or optimized within the past five years.

scholarly journals A database of high-resolution MS/MS spectra for lichen metabolites

2019 ◽  
Vol 6 (1) ◽  
Author(s):  
Damien Olivier-Jimenez ◽  
Marylène Chollet-Krugler ◽  
David Rondeau ◽  
Mehdi A. Beniddir ◽  
Solenn Ferron ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Gold Standard ◽  
Analytical Techniques ◽  
Liquid Chromatography Mass Spectrometry ◽  
Chemical Profiling ◽  
Botanical Museum ◽  
Versatile Tool ◽  
Technical Validation ◽  
Lichen Metabolites ◽  
Layer Chromatography

AbstractWhile analytical techniques in natural products research massively shifted to liquid chromatography-mass spectrometry, lichen chemistry remains reliant on limited analytical methods, Thin Layer Chromatography being the gold standard. To meet the modern standards of metabolomics within lichenochemistry, we announce the publication of an open access MS/MS library with 250 metabolites, coined LDB for Lichen DataBase, providing a comprehensive coverage of lichen chemodiversity. These were donated by the Berlin Garden and Botanical Museum from the collection of Siegfried Huneck to be analyzed by LC-MS/MS. Spectra at individual collision energies were submitted to MetaboLights (https://www.ebi.ac.uk/metabolights/MTBLS999) while merged spectra were uploaded to the GNPS platform (CCMSLIB00004751209 to CCMSLIB00004751517). Technical validation was achieved by dereplicating three lichen extracts using a Molecular Networking approach, revealing the detection of eleven unique molecules that would have been missed without LDB implementation to the GNPS. From a chemist’s viewpoint, this database should help streamlining the isolation of formerly unreported metabolites. From a taxonomist perspective, the LDB offers a versatile tool for the chemical profiling of newly reported species.

Metabolomic characterisation of the functional division of nitrogen metabolism in variegated leaves

2012 ◽  
Vol 39 (12) ◽  
pp. 959 ◽  
Author(s):  
Guillaume Tcherkez ◽  
Florence Guérard ◽  
Françoise Gilard ◽  
Marlène Lamothe ◽  
Caroline Mauve ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Biological Significance ◽  
Isotope Ratio Mass Spectrometry ◽  
Liquid Chromatography Mass Spectrometry ◽  
Isotopic Labelling ◽  
Green Areas ◽  
N Metabolism ◽  
Isotopic Measurements ◽  
Metabolic Exchange

Many horticultural and natural plant species have variegated leaves, that is, patchy leaves with green and non-green or white areas. Specific studies on the metabolism of variegated leaves are scarce and although white (non-green) areas have been assumed to play the role of a ‘nitrogen store’, there is no specific studies showing the analysis of nitrogenous metabolites and the dynamics of nitrogen assimilation. Here, we examined the metabolism of variegated leaves of Pelargonium × hortorum. We show that white areas have a larger N : C ratio, more amino acids, with a clear accumulation of arginine. Metabolomic analyses revealed clear differences in the chemical composition, suggesting contrasted metabolic commitments such as an enhancement of alkaloid biosynthesis in white areas. Using isotopic labelling followed by nuclear magnetic resonance or liquid chromatography/mass spectrometry, we further showed that in addition to glutamine, tyrosine and tryptophan, N metabolism forms ornithine in green area and huge amounts of arginine in white areas. Fine isotopic measurements with isotope ratio mass spectrometry indicated that white and green areas exchange nitrogenous molecules but nitrogen export from green areas is quantitatively much more important. The biological significance of the metabolic exchange between leaf areas is briefly discussed.

scholarly journals Neuropeptidomics: Improvements in Mass Spectrometry Imaging Analysis and Recent Advancements

2020 ◽  
Vol 21 ◽  
Author(s):  
Nhu Q. Vu ◽  
Kellen DeLaney ◽  
Lingjun Li
Keyword(s):  
Mass Spectrometry ◽  
Sample Preparation ◽  
Functional Role ◽  
Mass Spectrometry Imaging ◽  
Analytical Techniques ◽  
Model Organisms ◽  
Preparation Technique ◽  
Single Experiment ◽  
Recent Developments ◽  
Msi Analysis

: Neuropeptides are an important class of endogenous peptides in the nervous system that regulate physiological functions such as feeding, glucose homeostasis, pain, memory, reproduction, and many others. In order to understand the functional role of neuropeptides in diseases or disorders, studies investigating their dysregulation in terms of changes in abundance and localization must be carried out. Because multiple neuropeptides are believed to play a functional role in each physiological process, techniques capable of globally profiling multiple neuropeptides simultaneously are desired. Mass spectrometry is well-suited for this goal due to its ability to perform untargeted measurements without prior comprehensive knowledge of the analytes of interest. Mass spectrometry imaging (MSI) is particularly useful because it has the capability to image a large variety of peptides in a single experiment without labeling. Like all analytical techniques, careful sample preparation is critical to successful MSI analysis. The first half of this review focuses on recent developments in MSI sample preparation and instrumentation for analyzing neuropeptides and other biomolecules in which the sample preparation technique may be directly applicable for neuropeptide analysis. The benefit offered by incorporating these techniques is shown as improvement in number of observable neuropeptides, enhanced signal to noise, increased spatial resolution, or a combination of these aspects. The second half of this review focuses on recent biological discoveries about neuropeptides resulting from these improvements in MSI analysis. The recent progress in neuropeptide detection and analysis methods, including incorporation of various tissue washes, matrices, instruments, ionization sources, and computation approaches combined with the advancements in understanding neuropeptide function in a variety of model organisms indicates potential for the utilization of MSI analysis of neuropeptides in clinical settings.

scholarly journals Co-Culture Systems for the Production of Secondary Metabolites: Current and Future Prospects

2019 ◽  
Vol 13 (1) ◽  
pp. 18-26 ◽  
Author(s):  
Zin Quat Tan ◽  
Hui Yin Leow ◽  
David Charles Weerasingam Lee ◽  
Kanakeswary Karisnan ◽  
Adelene Ai Lian Song ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Antimicrobial Activity ◽  
Secondary Metabolites ◽  
Analytical Techniques ◽  
Liquid Chromatography Mass Spectrometry ◽  
Future Prospects ◽  
Culture Methods ◽  
Primary And Secondary Metabolites ◽  
Specificity And Sensitivity ◽  
Current Systems

Microorganisms are the great sources of Natural Products (NPs); these are imperative to their survival apart from conferring competitiveness amongst each other within their environmental niches. Primary and secondary metabolites are the two major classes of NPs that help in cell development, where antimicrobial activity is closely linked with secondary metabolites. To capitalize on the effects of secondary metabolites, co-culture methods have been often used to develop an artificial microbial community that promotes the action of these metabolites. Different analytical techniques will subsequently be employed based on the metabolite specificity and sensitivity to further enhance the metabolite induction. Liquid Chromatography-Mass Spectrometry (LC-MS) and Gas Chromatography (GC)-MS are commonly used for metabolite separation while Nuclear Magnetic Resonance (NMR) and Mass Spectrometry (MS) have been used as tools to elucidate the structure of compounds. This review intends to discuss current systems in use for co-culture in addition to its advantages, with discourse into the investigation of specific techniques in use for the detailed study of secondary metabolites. Further advancements and focus on co-culture technologies are required to fully realize the massive potential in synthetic biological systems.

Corrigendum to: Metabolomic characterisation of the functional division of nitrogen metabolism in variegated leaves

2014 ◽  
Vol 41 (3) ◽  
pp. 330
Author(s):  
Guillaume Tcherkez ◽  
Florence Guérard ◽  
Françoise Gilard ◽  
Marlène Lamothe ◽  
Caroline Mauve ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Biological Significance ◽  
Isotope Ratio Mass Spectrometry ◽  
Liquid Chromatography Mass Spectrometry ◽  
Isotopic Labelling ◽  
Green Areas ◽  
N Metabolism ◽  
Isotopic Measurements ◽  
Metabolic Exchange

Many horticultural and natural plant species have variegated leaves, that is, patchy leaves with green and non-green or white areas. Specific studies on the metabolism of variegated leaves are scarce and although white (non-green) areas have been assumed to play the role of a ‘nitrogen store', there is no specific studies showing the analysis of nitrogenous metabolites and the dynamics of nitrogen assimilation. Here, we examined the metabolism of variegated leaves of Pelargonium × hortorum. We show that white areas have a larger N : C ratio, more amino acids, with a clear accumulation of arginine. Metabolomic analyses revealed clear differences in the chemical composition, suggesting contrasted metabolic commitments such as an enhancement of alkaloid biosynthesis in white areas. Using isotopic labelling followed by nuclear magnetic resonance or liquid chromatography/mass spectrometry, we further showed that in addition to glutamine, tyrosine and tryptophan, N metabolism forms ornithine in green area and huge amounts of arginine in white areas. Fine isotopic measurements with isotope ratio mass spectrometry indicated that white and green areas exchange nitrogenous molecules but nitrogen export from green areas is quantitatively much more important. The biological significance of the metabolic exchange between leaf areas is briefly discussed.

Sign in / Sign up

Export Citation Format

Share Document