Multi-omics analysis delineates the distinct functions of sub-cellular acetyl-CoA pools in Toxoplasma gondii

Abstract

Background Acetyl-CoA is a key molecule in all organisms, implicated in several metabolic pathways as well as in transcriptional regulation and post-translational modification. The human pathogen Toxoplasma gondii possesses at least four enzymes which generate acetyl-CoA in the nucleo-cytosol (acetyl-CoA synthetase (ACS); ATP citrate lyase (ACL)), mitochondrion (branched-chain α-keto acid dehydrogenase-complex (BCKDH)) and apicoplast (pyruvate dehydrogenase complex (PDH)). Given the diverse functions of acetyl-CoA, we know very little about the role of sub-cellular acetyl-CoA pools in parasite physiology. Results To assess the importance and functions of sub-cellular acetyl-CoA-pools, we measured the acetylome, transcriptome, proteome and metabolome of parasites lacking ACL/ACS or BCKDH. We demonstrate that ACL/ACS constitute a synthetic lethal pair. Loss of both enzymes causes a halt in fatty acid elongation, hypo-acetylation of nucleo-cytosolic and secretory proteins and broad changes in gene expression. In contrast, loss of BCKDH results in an altered TCA cycle, hypo-acetylation of mitochondrial proteins and few specific changes in gene expression. We provide evidence that changes in the acetylome, transcriptome and proteome of cells lacking BCKDH enable the metabolic adaptations and thus the survival of these parasites. Conclusions Using multi-omics and molecular tools, we obtain a global and integrative picture of the role of distinct acetyl-CoA pools in T. gondii physiology. Cytosolic acetyl-CoA is essential and is required for the synthesis of parasite-specific fatty acids. In contrast, loss of mitochondrial acetyl-CoA can be compensated for through metabolic adaptations implemented at the transcriptional, translational and post-translational level.

Untargeted Metabolomics Uncovers the Essential Lysine Transporter in Toxoplasma gondii

“…Two additional studies have previously localized endogenously tagged TGME49_240810 to the plasma membrane [ 11 , 19 ]. While T. gondii secretes some metabolic end products across the plasma membrane, including lactate, alanine, and succinate, the list of secreted metabolites is relatively short, and the lactate transporters have been identified and characterized [ 20 , 21 , 22 ]. Thus, TGME49_240810, here referred to as AT6-1 [ 11 ], was considered a strong candidate for a transporter facilitating the uptake of an essential metabolite across the parasite plasma membrane.…”

“…Plaque assays and growth assays were carried out as described previously [ 21 , 38 ]. In brief: for plaque assays, different dilutions of parasite cultures were incubated on a confluent host cells monolayer for 7 days.…”

Preclinical characterization and target validation of the antimalarial pantothenamide MMV693183

“…Here, we have conclusively demonstrated for the first time that CoA-PanAm is the active metabolite that inhibits ACS. With the previously suggested role of ACS in regulating the acetylome, transcriptome and metabolome (including fatty acid elongation) (27,28,30,31,39) and the corresponding cytoplasmic/perinuclear (this study) and nuclear localization of ACS for these functions (31), it could be hypothesized that these pathways are affected by CoA-PanAms.…”

“…ACS is predicted to provide acetyl-CoA for a variety of processes in the parasite, including fatty acid elongation in the endoplasmic reticulum and post-translational modifications in the cytosol and nucleus (27)(28)(29). To begin to explore whether inhibition of ACS could affect these downstream pathways, we studied the localization of ACS using an endogenous GFP-tagged ACS parasite line (Fig S9a-b).…”

Systematic Review of Multi-Omics Approaches to Investigate Toxicological Effects in Macrophages

“…Due to the enhancement of omics approaches and strategies for multi-omics data integration over the last years, we believe that this needs to be changed in the future. Thereby, not only the integration of transcriptome, proteome, and metabolome but also of further omics layers, e.g., epigenome [ 176 ], methylome [ 177 ], acetylome [ 178 ], and phosphoproteome [ 179 ], should be considered. Post-translational modifications (PTMs) are highly relevant since they regulate protein function, activity and thus, cell signaling [ 180 ].…”