PI3K drives the de novo synthesis of coenzyme A from vitamin B5

Abstract

In response to hormones and growth factors, the class I phosphoinositide-3-kinase (PI3K) signalling network functions as a major regulator of metabolism and growth, governing cellular nutrient uptake, energy generation, reducing cofactor production and macromolecule biosynthesis1. Many of the driver mutations in cancer with the highest recurrence, including in receptor tyrosine kinases, Ras, PTEN and PI3K, pathologically activate PI3K signalling2,3. However, our understanding of the core metabolic program controlled by PI3K is almost certainly incomplete. Here, using mass-spectrometry-based metabolomics and isotope tracing, we show that PI3K signalling stimulates the de novo synthesis of one of the most pivotal metabolic cofactors: coenzyme A (CoA). CoA is the major carrier of activated acyl groups in cells4,5 and is synthesized from cysteine, ATP and the essential nutrient vitamin B5 (also known as pantothenate)6,7. We identify pantothenate kinase 2 (PANK2) and PANK4 as substrates of the PI3K effector kinase AKT8. Although PANK2 is known to catalyse the rate-determining first step of CoA synthesis, we find that the minimally characterized but highly conserved PANK49 is a rate-limiting suppressor of CoA synthesis through its metabolite phosphatase activity. Phosphorylation of PANK4 by AKT relieves this suppression. Ultimately, the PI3K–PANK4 axis regulates the abundance of acetyl-CoA and other acyl-CoAs, CoA-dependent processes such as lipid metabolism and proliferation. We propose that these regulatory mechanisms coordinate cellular CoA supplies with the demands of hormone/growth-factor-driven or oncogene-driven metabolism and growth.

Metabolic adaptations underpin resistance to histone acetyltransferase inhibition

“…7d) . PANK4 dephosphorylates 4’-phosphopantetheine, an intermediate metabolite of CoA biosynthesis, to antagonize CoA biosynthesis 7 . We confirmed that genetic disruption of PANK4 conferred a competitive growth advantage under selective pressure from CBP/p300 HAT inhibition and clonal expansions of the MOLM-13 cells with PANK4 knockouts displayed diminished sensitivity to CBP/p300 HAT inhibition by A-485 (Fig.…”

“…We further validated these results using a genome-scale CRISPR/Cas9 loss-of-function genetic modifier screen, which identified additional gene-drug interactions between HAT inhibitors and the CoA biosynthetic pathway. Top hits from the screen included the phosphatase, PANK4 , which negatively regulates CoA production and therefore suppresses sensitivity to HAT inhibition upon knockout 7 , as well as the pantothenate transporter, SLC5A6 8 , which enhances sensitivity. Altogether, this work uncovers CoA plasticity as an unexpected but potentially class-wide liability of anti-cancer HAT inhibitors and will therefore buoy future efforts to optimize the efficacy of this new form of targeted therapy.…”

Generation and Validation of an Anti-Human PANK3 Mouse Monoclonal Antibody

“…Pantothenate kinases, a family of four evolutionarily conserved proteins, regulate the de-novo CoA biosynthesis in prokaryotes as well as eukaryotes [ 5 ]. The family of PANKs constitutes four catalytically active kinases: nuclear PANK1α and cytosolic PANK1β (both encoded by PANK1 ); mitochondrial (intermembrane space) PANK2; cytosolic PANK3; and a phosphatase—cytosolic PANK4 [ 6 , 7 ]. As the rate-limiting enzymes of the pathway, PANK1, 2, and 3 phosphorylate pantothenic acid (vitamin B 5 ), which is converted into CoA in a series of four evolutionarily conserved enzymatic reactions, while PANK4 negatively regulates CoA synthesis by dephosphorylation of the pathway metabolites [ 6 , 7 , 8 ].…”

“…The family of PANKs constitutes four catalytically active kinases: nuclear PANK1α and cytosolic PANK1β (both encoded by PANK1 ); mitochondrial (intermembrane space) PANK2; cytosolic PANK3; and a phosphatase—cytosolic PANK4 [ 6 , 7 ]. As the rate-limiting enzymes of the pathway, PANK1, 2, and 3 phosphorylate pantothenic acid (vitamin B 5 ), which is converted into CoA in a series of four evolutionarily conserved enzymatic reactions, while PANK4 negatively regulates CoA synthesis by dephosphorylation of the pathway metabolites [ 6 , 7 , 8 ]. PANK isoforms are also differentially expressed and regulated, enabling these proteins to sense and maintain the levels of CoA and its thioesters differentially in a specific cellular compartment [ 2 , 9 ].…”

Genetic depletion of de novo coenzyme A biosynthesis exacerbates puromycin toxicity

“…In prokaryotes as well as higher eukaryotes, denovo CoA synthesis occurs from pantothenate, with the first and rate limiting step catalyzed by the pantothenate kinase (PANK) family of enzymes (Figure 1B) (22,23). Three PANK enzymes catalyze the conversion of pantothenate to 4'-phosphopantothenate (PANK1, 2, and 3), with PANK4 retaining phosphatase activity that is suggested to be critical in constraining cellular CoA concentration (22)(23)(24)(25). Our investigations on CoA biosynthesis as a potential targetable vulnerability in cancers led us to assess whether genetic manipulation of the pantothenate kinases PANK 1, 2 and 3, as the key regulatory enzymes of de-novo CoA biosynthesis in prokaryotes and eukaryotes, could impact cancer cell viability.…”