TY - JOUR
T1 - Multi-Omic Analysis to Characterize Metabolic Adaptation of the E. coli Lipidome in Response to Environmental Stress
AU - Kralj, Thomas
AU - Nuske, Madison
AU - Hofferek, Vinzenz
AU - Sani, Marc Antoine
AU - Lee, Tzong Hsien
AU - Separovic, Frances
AU - Aguilar, Marie Isabel
AU - Reid, Gavin E.
N1 - Funding Information:
Funding: This research was funded by the National Health and Medical Research Council, grant number APP1142750 (G.E.R., F.S., and M.-I.A.), and by the Australian Research Council, grant number DP190102464 (G.E.R). The APC was funded from DP190102464. The authors acknowledge support from Dr. Romain Huguet (Thermo Fisher Scientific, San Jose, CA, USA) for providing the FAIMS Pro source and the 213 nm UV laser used in this study as part of a collaborative research project with G.E.R.
Publisher Copyright:
© 2022 by the authors. Licensee MDPI, Basel, Switzerland.
PY - 2022/2
Y1 - 2022/2
N2 - As an adaptive survival response to exogenous stress, bacteria undergo dynamic remod-elling of their lipid metabolism pathways to alter the composition of their cellular membranes. Here, using Escherichia coli as a well characterised model system, we report the development and application of a ‘multi-omics’ strategy for comprehensive quantitative analysis of the temporal changes in the lipidome and proteome profiles that occur under exponential growth phase versus stationary growth phase conditions i.e., nutrient depletion stress. Lipidome analysis performed using ‘shot-gun’ direct infusion-based ultra-high resolution accurate mass spectrometry revealed a quantitative decrease in total lipid content under stationary growth phase conditions, along with a significant increase in the mol% composition of total cardiolipin, and an increase in ‘odd-numbered’ acyl-chain length containing glycerophospholipids. The inclusion of field asymmetry ion mobility spectrometry was shown to enable the enrichment and improved depth of coverage of low-abundance cardiolip-ins, while ultraviolet photodissociation-tandem mass spectrometry facilitated more complete lipid structural characterisation compared with conventional collision-induced dissociation, including unambiguous assignment of the odd-numbered acyl-chains as containing cyclopropyl modifications. Proteome analysis using data-dependent acquisition nano-liquid chromatography mass spectrometry and tandem mass spectrometry analysis identified 83% of the predicted E. coli lipid metabolism enzymes, which enabled the temporal dependence associated with the expression of key enzymes responsible for the observed adaptive lipid metabolism to be determined, including those involved in phospholipid metabolism (e.g., ClsB and Cfa), fatty acid synthesis (e.g., FabH) and degradation (e.g., FadA/B,D,E,I,J and M), and proteins involved in the oxidative stress response resulting from the generation of reactive oxygen species during β-oxidation or lipid degradation.
AB - As an adaptive survival response to exogenous stress, bacteria undergo dynamic remod-elling of their lipid metabolism pathways to alter the composition of their cellular membranes. Here, using Escherichia coli as a well characterised model system, we report the development and application of a ‘multi-omics’ strategy for comprehensive quantitative analysis of the temporal changes in the lipidome and proteome profiles that occur under exponential growth phase versus stationary growth phase conditions i.e., nutrient depletion stress. Lipidome analysis performed using ‘shot-gun’ direct infusion-based ultra-high resolution accurate mass spectrometry revealed a quantitative decrease in total lipid content under stationary growth phase conditions, along with a significant increase in the mol% composition of total cardiolipin, and an increase in ‘odd-numbered’ acyl-chain length containing glycerophospholipids. The inclusion of field asymmetry ion mobility spectrometry was shown to enable the enrichment and improved depth of coverage of low-abundance cardiolip-ins, while ultraviolet photodissociation-tandem mass spectrometry facilitated more complete lipid structural characterisation compared with conventional collision-induced dissociation, including unambiguous assignment of the odd-numbered acyl-chains as containing cyclopropyl modifications. Proteome analysis using data-dependent acquisition nano-liquid chromatography mass spectrometry and tandem mass spectrometry analysis identified 83% of the predicted E. coli lipid metabolism enzymes, which enabled the temporal dependence associated with the expression of key enzymes responsible for the observed adaptive lipid metabolism to be determined, including those involved in phospholipid metabolism (e.g., ClsB and Cfa), fatty acid synthesis (e.g., FabH) and degradation (e.g., FadA/B,D,E,I,J and M), and proteins involved in the oxidative stress response resulting from the generation of reactive oxygen species during β-oxidation or lipid degradation.
KW - E. coli
KW - Environmental stress
KW - Ion mobility
KW - Lipidome
KW - Mass spectrometry
KW - Photodissociation
KW - Proteome
UR - http://www.scopus.com/inward/record.url?scp=85124827672&partnerID=8YFLogxK
U2 - 10.3390/metabo12020171
DO - 10.3390/metabo12020171
M3 - Article
C2 - 35208246
AN - SCOPUS:85124827672
SN - 2218-1989
VL - 12
JO - Metabolites
JF - Metabolites
IS - 2
M1 - 171
ER -