Continuous in vivo Metabolism by NMR

Abstract

Dense time-series metabolomics data are essential for unraveling the underlying dynamic properties of metabolism. Here we extend high-resolution-magic angle spinning (HR-MAS) to enable continuous in vivo monitoring of metabolism by NMR (CIVM-NMR) and provide analysis tools for these data. First, we reproduced a result in human chronic lymphoid leukemia cells by using isotope-edited CIVM-NMR to rapidly and unambiguously demonstrate unidirectional flux in branched-chain amino acid metabolism. We then collected untargeted CIVM-NMR datasets for Neurospora crassa , a classic multicellular model organism, and uncovered dynamics between central carbon metabolism, amino acid metabolism, energy storage molecules, and lipid and cell wall precursors. Virtually no sample preparation was required to yield a dynamic metabolic fingerprint over hours to days at ~4-min temporal resolution with little noise. CIVM-NMR is simple and readily adapted to different types of cells and microorganisms, offering an experimental complement to kinetic models of metabolism for diverse biological systems.

Catch the wave: Metabolomic analyses in human pathogenic fungi

“…Further, new advances in the metabolomics field should be considered. For instance, Judge and colleagues used Neurospora crassa as a model organism for continuous in vivo monitoring of fungal metabolism [ 7 ]. In another study, antifungal drug activity was monitored in vivo and experimentally validated in A .…”

“…Mass spectrometry (MS) and nucleic magnetic resonance (NMR) are the analytical tools of choice in most metabolomic studies, with a plethora of substrate-and study-specific variations available [1][2][3]. An overview of the most commonly used techniques and critical points to consider during study design is presented in Fig 1. Such approaches have been utilized in fungal research to perform untargeted monitoring of primary and secondary metabolites (SMs), targeted search for biomarkers (e.g., lipidomics), and in vivo measurement of metabolic fluxes [4][5][6][7]. For downstream analysis of metabolomic data, an increasing number of databases, software, and tools are available (summarized in [8,9]).…”

Single Cell Metabolomics: A Future Tool to Unmask Cellular Heterogeneity and Virus-Host Interaction in Context of Emerging Viral Diseases

“…However requirement of large sample volume and the issue of sensitivity render it imperfect for SCM analyses rather it is preferred for tissue sample and biofluid introspection. For example continuous in vivo metabolism has been followed by using NMR (CIVM-NMR) coupled with highresolution-magic angle spinning to elucidate branched-chain amino acid metabolism in human chronic lymphoid leukemia cells (Judge et al, 2019).…”

RTExtract: time-series NMR spectra quantification based on 3D surface ridge tracking

“…Experimental approaches have been developed in time-series metabolic measurements by both nuclear magnetic resonance (NMR) and mass spectrometry ( Bastawrous et al ., 2018 ; Judge et al ., 2019 ; Koczula et al ., 2016 ; Link et al ., 2015 ; Montana et al ., 2011 ; Tabatabaei Anaraki et al ., 2018 ). These experimental methods provide opportunities to understand metabolic dynamics, including metabolic changes under variation in carbon sources or oxygen levels ( Judge et al ., 2019 ; Link et al ., 2014 , 2015 ). Among existing approaches, continuous in vivo monitoring of metabolism by NMR (CIVM-NMR) provided high time resolution, in vivo measurements of metabolites in Neurospora crassa under aerobic and anaerobic conditions ( Judge et al ., 2019 ).…”

“…These experimental methods provide opportunities to understand metabolic dynamics, including metabolic changes under variation in carbon sources or oxygen levels ( Judge et al ., 2019 ; Link et al ., 2014 , 2015 ). Among existing approaches, continuous in vivo monitoring of metabolism by NMR (CIVM-NMR) provided high time resolution, in vivo measurements of metabolites in Neurospora crassa under aerobic and anaerobic conditions ( Judge et al ., 2019 ). These measurements covered a large proportion of pathways in central metabolism, and interesting dynamics in compound concentration were observed.…”