bims-medhac 2020-06-21 papers

Issue of 2020‒06‒21
four papers selected by
Alessandro Carrer
Veneto Institute of Molecular Medicine

BMC Biol. 2020 Jun 16. 18(1): 67

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

Joachim Kloehn, Rebecca D Oppenheim, Ghizal Siddiqui, Pieter-Jan De Bock, Sunil Kumar Dogga, Yohann Coute, Mohamed-Ali Hakimi, Darren J Creek, Dominique Soldati-Favre.

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.

Keywords: ATP citrate lyase (ACL); Acetyl-CoA; Acetyl-CoA synthetase (ACS); Acetylome; Branched-chain α-keto acid dehydrogenase-complex (BCKDH); Formate/nitrite transporter (FNT); Metabolism; Multi-omics; Phosphoenolpyruvate carboxykinase (PEPCK); Toxoplasma gondii

DOI: https://doi.org/10.1186/s12915-020-00791-7

Nat Commun. 2020 Jun 19. 11(1): 3148

Leucine regulates autophagy via acetylation of the mTORC1 component raptor.

Sung Min Son, So Jung Park, Eleanna Stamatakou, Mariella Vicinanza, Fiona M Menzies, David C Rubinsztein.

Macroautophagy ("autophagy") is the main lysosomal catabolic process that becomes activated under nutrient-depleted conditions, like amino acid (AA) starvation. The mechanistic target of rapamycin complex 1 (mTORC1) is a well-conserved negative regulator of autophagy. While leucine (Leu) is a critical mTORC1 regulator under AA-starved conditions, how Leu regulates autophagy is poorly understood. Here, we describe that in most cell types, including neurons, Leu negatively regulates autophagosome biogenesis via its metabolite, acetyl-coenzyme A (AcCoA). AcCoA inhibits autophagy by enhancing EP300-dependent acetylation of the mTORC1 component raptor, with consequent activation of mTORC1. Interestingly, in Leu deprivation conditions, the dominant effects on autophagy are mediated by decreased raptor acetylation causing mTORC1 inhibition, rather than by altered acetylation of other autophagy regulators. Thus, in most cell types we examined, Leu regulates autophagy via the impact of its metabolite AcCoA on mTORC1, suggesting that AcCoA and EP300 play pivotal roles in cell anabolism and catabolism.

DOI: https://doi.org/10.1038/s41467-020-16886-2

Gene X. 2020 Dec;5 100034

Glucose and TNF enhance expression of TNF and IL1B, and histone H3 acetylation and K4/K36 methylation, in juvenile macrophage cells.

Kazue Honma, Chie Machida, Kazuki Mochizuki, Toshinao Goda.

Hyperglycemia activates innate leukocytes such as monocytes and induces pro-inflammatory cytokine expression, resulting in increased monocyte adhesion to aortic endothelial cells. In this study, we investigated whether high glucose and/or tumor necrosis factor (TNF) would enhance pro-inflammatory cytokine expression of tumor necrosis factor (TNF) and interleukin (IL)-1β (IL1B) by altering histone modifications in U937, a juvenile macrophage cell line. The mRNA levels of TNF and IL1B in U937 cells were significantly affected by glucose concentration and TNF treatment. Mono-methylated histone H3K4 signals around TNF and IL1B were lower in cells treated with high glucose compared with low glucose. Conversely, tri-methylated histone H3K4 and H3K36 signals were higher in cells treated with high glucose compared with low glucose. TNF treatment of U937 cells cultured in high glucose enhanced histone H3K36 tri-methylation, particularly around the gene regions of TNF and IL1B. Histone acetylation was induced by treatment with TNF in high-glucose medium. The induction of acetylation and tri-methylation of K4 and K36 of histone H3 around TNF and IL1B by treatment with high glucose and/or TNF was positively associated with the induction of these genes in juvenile macrophage U937 cells.

Keywords: CHD1, chromo-ATPase/helicase-DNA binding domain 1; ChIP, chromatin immunoprecipitation; FCS, fetal calf serum; H3K36 methylation; H3K4 methylation; Histone acetylation; IL, interleukin; Juvenile macrophage; P-TEFb, positive transcription elongation factor b; Pro-inflammatory cytokine; ROS, reactive oxygen species; TNF, tumor necrosis factor; U937

DOI: https://doi.org/10.1016/j.gene.2020.100034

Exp Hematol Oncol. 2020 ;9 12

Development of human prostate cancer stem cells involves epigenomic alteration and PI3K/AKT pathway activation.

Jingjing Wu, Shundong Cang, Christina Liu, Whitman Ochiai, Jen Wei Chiao.

Background: Human prostate cancer spheres endowed with stem cell properties have been obtained from androgen-dependent cell line LNCaP after exposure to an epigenomic modulator phenethyl isothiocynate (PEITC). Sphere cells can self-renew and grow with androgen, and also without androgen. Little is known about the signaling pathway and mechanism in the development of the stem cells in the spheres.Methods: Expression of phosphoinositol-3 kinase (PI3K) pathway members and histone acetylation were quantified in the tumor spheres and LNCaP cells by western immunoblotting.
Results: The level of phosphorylated AKT was significantly increased in the sphere stem cells than the LNCaP cells at an average of 7.4 folds (range 5.8-10.7 folds), whereas the P27 level was elevated 5.4 folds (range 4.8-6.3 folds) (P < 0.05). The acetylation level on histone H3 lysine 9 was decreased.
Conclusions: PEITC appears to regulate the epigenome through histone acetylation and activate the PI3K/AKT pathway in the LNCaP cells. This mechanism may be responsible in part for the development of the prostate cancer stem cells.

Keywords: AKT; Cancer stem cells; Histone acetylation; PI3K; Prostate cancer; Sphere

DOI: https://doi.org/10.1186/s40164-020-00168-0