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  • Inferring Active Metabolic Pathways from Proteomics and Essentiality Data.

Inferring Active Metabolic Pathways from Proteomics and Essentiality Data.

Cell reports (2020-06-04)
Ariadna Montero-Blay, Carlos Piñero-Lambea, Samuel Miravet-Verde, Maria Lluch-Senar, Luis Serrano
ABSTRACT

Here, we propose an approach to identify active metabolic pathways by integrating gene essentiality analysis and protein abundance. We use two bacterial species (Mycoplasma pneumoniae and Mycoplasma agalactiae) that share a high gene content similarity yet show significant metabolic differences. First, we build detailed metabolic maps of their carbon metabolism, the most striking difference being the absence of two key enzymes for glucose metabolism in M. agalactiae. We then determine carbon sources that allow growth in M. agalactiae, and we introduce glucose-dependent growth to show the functionality of its remaining glycolytic enzymes. By analyzing gene essentiality and performing quantitative proteomics, we can predict the active metabolic pathways connected to carbon metabolism and show significant differences in use and direction of key pathways despite sharing the large majority of genes. Gene essentiality combined with quantitative proteomics and metabolic maps can be used to determine activity and directionality of metabolic pathways.

MATERIALS
Product Number
Brand
Product Description

Sigma-Aldrich
Sodium pyruvate, ReagentPlus®, ≥99%
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L-(+)-Lactic acid solution, in H2O, ≥85%
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D-(−)-Ribose, 98%
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D-(+)-Mannose, powder, BioReagent, suitable for cell culture
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Glycerol, for molecular biology, ≥99.0%
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D-(−)-Fructose, ≥99% (HPLC)
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L-Ascorbic acid, reagent grade
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L-Arginine, reagent grade, ≥98%