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The ATP:ADP ratio is a critical parameter of cellular energy status that regulates many metabolic activities. Here we report an optimized genetically encoded fluorescent biosensor, PercevalHR, that senses the ATP:ADP ratio. PercevalHR is tuned to the range of intracellular ATP:ADP expected in mammalian cells, and it can be used with one- or two-photon microscopy in live samples. We use PercevalHR to visualize activity-dependent changes in ATP:ADP when neurons are exposed to multiple stimuli, demonstrating that it is a sensitive reporter of physiological changes in energy consumption and production. We also use PercevalHR to visualize intracellular ATP:ADP while simultaneously recording currents from ATP-sensitive potassium (K ATP ) channels in single cells, showing that PercevalHR enables the study of coordinated variation in ATP:ADP and K ATP channel open probability in intact cells. With its ability to monitor changes in cellular energetics within seconds, PercevalHR should be a versatile tool for metabolic research. The ratio between ATP and ADP within the cell is a key indicator of metabolic status. Tantama et al . describe a ratiometric, genetically encoded fluorescent sensor for ATP:ADP that is now optimized for mammalian cells, and demonstrate that it can detect physiological changes in energy consumption and production.

Inorganic polyphosphate (polyP) is a linear polymer of tens or hundreds of phosphate residues linked by high-energy bonds. It is found in all organisms and has been proposed to serve as an energy source in a pre-ATP world. This ubiquitous and abundant biopolymer plays numerous and vital roles in metabolism and regulation in prokaryotes and eukaryotes, but the underlying molecular mechanisms for most activities of polyP remain unknown. In prokaryotes, the synthesis and utilization of polyP are catalyzed by 2 families of polyP kinases, PPK1 and PPK2, and polyphosphatases. Here, we present structural and functional characterization of the PPK2 family. Proteins with a single PPK2 domain catalyze polyP-dependent phosphorylation of ADP to ATP, whereas proteins containing 2 fused PPK2 domains phosphorylate AMP to ADP. Crystal structures of 2 representative proteins, SMc02148 from Sinorhizobium meliloti and PA3455 from Pseudomonas aeruginosa, revealed a 3-layer α/β/α sandwich fold with an α-helical lid similar to the structures of microbial thymidylate kinases, suggesting that these proteins share a common evolutionary origin and catalytic mechanism. Alanine replacement mutagenesis identified 9 conserved residues, which are required for activity and include the residues from both Walker A and B motifs and the lid. Thus, the PPK2s represent a molecular mechanism, which potentially allow bacteria to use polyP as an intracellular energy reserve for the generation of ATP and survival.

Melanoma immunotherapy is still not satisfactory due to immunosuppressive cell populations within the tumor stroma. Targeting tumor-associated macrophages (TAM) can help to restore an anti-tumor immunity. Previously, we could show that classical TAM markers expressed in vivo need a 7 day M-CSF/dexamethasone/IL-4 (MDI) stimulation for their induction in peripheral blood monocytes (pBM) in vitro. To identify possible novel therapeutic targets on TAM, gene expression analysis of MDI-treated pBM was performed. This identified up-regulation of the purinergic G-protein coupled receptor P2Y12, the therapeutic target of the clinically approved anti-thrombotic drugs cangrelor, clopidogrel, ticagrelor, and prasugrel. We generated a peptide antibody and validated its specificity using transgenic P2Y12 + U937 cells. With the help of this antibody, P2Y12 expression was confirmed on CD68 + CD163 + TAM of melanoma in situ. Functional analysis revealed that treatment of transgenic P2Y12 + U937 cells with the receptor agonist 2-MeSADP induced ERK1/2 and Akt phosphorylation and increased the secretion of the chemokines CXCL2, CXCL7, and CXCL8. These effects could be abolished with the P2Y12 antagonist PSB0739 or with Akt and ERK inhibitors. In addition, P2Y12 + macrophages migrated towards the ADP-rich culture medium of puromycin-treated dying B16F1 melanoma cells. Cangrelor treatment blocked migration. Taken together, our results indicate that P2Y12 is an important chemotaxis receptor, which triggers migration of macrophages towards nucleotide-rich, necrotic tumor areas, and modulates the inflammatory environment upon ADP binding.

An emerging paradigm in enzymology is that transient high-energy structural states play crucial roles in enzymatic reaction cycles. Generally, these high-energy or ‘invisible’ states cannot be studied directly at atomic resolution using existing structural and spectroscopic techniques owing to their low populations or short residence times. Here we report the direct NMR-based detection of the molecular topology and conformational dynamics of a catalytically indispensable high-energy state of an adenylate kinase variant. On the basis of matching energy barriers for conformational dynamics and catalytic turnover, it was found that the enzyme’s catalytic activity is governed by its dynamic interconversion between the high-energy state and a ground state structure that was determined by X-ray crystallography. Our results show that it is possible to rationally tune enzymes’ conformational dynamics and hence their catalytic power—a key aspect in rational design of enzymes catalysing novel reactions. Adenylate kinase (AdK) plays a key role in cellular energy homeostasis by catalysing the reversible magnesium-dependent formation of ADP from AMP and ATP. Here the authors present a detailed analysis of adenylate kinase’s conformational dynamics and characterize a high-energy state of AdK indispensable for catalysis.

A novel poly(ADP-ribose)-binding zinc finger (PBZ) motif is identified. This motif is found in several eukaryotic checkpoint and DNA repair proteins, such as CHFR and APLF. Mutations in the PBZ of CHFR affect its function in checkpoint regulation, suggesting that both the poly (ADP-ribosyl)ation of proteins, and the interaction of this modification with other factors, is important for the DNA damage response. Post-translational modification (PTM) of proteins plays an important part in mediating protein interactions and/or the recruitment of specific protein targets 1 , 2 . PTM can be mediated by the addition of functional groups (for example, acetylation or phosphorylation), peptides (for example, ubiquitylation or sumoylation), or nucleotides (for example, poly(ADP-ribosyl)ation). Poly(ADP-ribosyl)ation often involves the addition of long chains of ADP-ribose units, linked by glycosidic ribose–ribose bonds 3 , and is critical for a wide range of processes, including DNA repair, regulation of chromosome structure, transcriptional regulation, mitosis and apoptosis 4 . Here we identify a novel poly(ADP-ribose)-binding zinc finger (PBZ) motif in a number of eukaryotic proteins involved in the DNA damage response and checkpoint regulation. The PBZ motif is also required for post-translational poly(ADP-ribosyl)ation. We demonstrate interaction of poly(ADP-ribose) with this motif in two representative human proteins, APLF (aprataxin PNK-like factor) and CHFR (checkpoint protein with FHA and RING domains), and show that the actions of CHFR in the antephase checkpoint are abrogated by mutations in PBZ or by inhibition of poly(ADP-ribose) synthesis.

The maintenance of genome stability and the prevention of genotoxic damage to DNA require immediate DNA repair. In the cell, the repair process is usually preceded by a release of DNA from complexes with chromatin proteins accompanied by nucleosome sliding, relaxing or disassembly. Base excision DNA repair (BER) corrects the most common DNA lesions, which does not disturb the DNA helix dramatically. Notably, small DNA lesions can be repaired in chromatin without global chromatin decompaction. One of the regulatory mechanisms is poly(ADP-ribosyl)ation, leading to the relaxation of the nucleosome. In our work, we demonstrated that recently a discovered protein, HPF1, can modulate the efficiency of one of the key BER stages—DNA synthesis—via the regulation of total poly(ADP-ribosyl)ation. Accordingly, we investigated both short-patch and long-patch DNA synthesis catalyzed by DNA polymerase β (pol β; main polymerase in BER) and showed that HPF1’s influence on the poly(ADP-ribosyl)ation catalyzed by PARP1 and especially by PARP2 results in more efficient DNA synthesis in the case of the short-patch BER pathway in nucleosomes. Additionally, HPF1-dependent poly(ADP-ribosyl)ation was found to positively regulate long-patch BER.

Uridine-cytidine kinase 2 is implicated in uncontrolled proliferation of abnormal cells and it is a hallmark of cancer, therefore, there is need for effective inhibitors of this key enzyme. In this study, we employed the used of in silico studies to find effective UCK2 inhibitors of natural origin using bioinformatics tools. An in vitro kinase assay was established by measuring the amount of ADP production in the presence of ATP and 5-fluorouridine as a substrate. Molecular docking studies revealed an interesting ligand interaction with the UCK2 protein for both flavokawain B and alpinetin. Both compounds were found to reduce ADP production, possibly by inhibiting UCK2 activity in vitro. In conclusion, we have identified flavokawain B and alpinetin as potential natural UCK2 inhibitors as determined by their interactions with UCK2 protein using in silico molecular docking studies. This can provide information to identify lead candidates for further drug design and development.

Long-term memory (LTM) formation requires new protein synthesis and new gene expression. Based on our work in Aplysia, we hypothesized that the rRNA genes, stimulation-dependent targets of the enzyme Poly(ADP-ribose) polymerase-1 (PARP-1), are primary effectors of the activity-dependent changes in synaptic function that maintain synaptic plasticity and memory. Using electrophysiology, immunohistochemistry, pharmacology and molecular biology techniques, we show here, for the first time, that the maintenance of forskolin-induced late-phase long-term potentiation (L-LTP) in mouse hippocampal slices requires nucleolar integrity and the expression of new rRNAs. The activity-dependent upregulation of rRNA, as well as L-LTP expression, are poly(ADP-ribosyl)ation (PAR) dependent and accompanied by an increase in nuclear PARP-1 and Poly(ADP) ribose molecules (pADPr) after forskolin stimulation. The upregulation of PARP-1 and pADPr is regulated by Protein kinase A (PKA) and extracellular signal-regulated kinase (ERK)--two kinases strongly associated with long-term plasticity and learning and memory. Selective inhibition of RNA Polymerase I (Pol I), responsible for the synthesis of precursor rRNA, results in the segmentation of nucleoli, the exclusion of PARP-1 from functional nucleolar compartments and disrupted L-LTP maintenance. Taken as a whole, these results suggest that new rRNAs (28S, 18S, and 5.8S ribosomal components)--hence, new ribosomes and nucleoli integrity--are required for the maintenance of long-term synaptic plasticity. This provides a mechanistic link between stimulation-dependent gene expression and the new protein synthesis known to be required for memory consolidation.

Conflicting reports have suggested that the silent information regulator 2 (SIR2) protein family employs NAD+to ADP-ribosylate histones [Tanny, J. C., Dowd, G. J., Huang, J., Hilz, H. & Moazed, D. (1999) Cell 99, 735-745; Frye, R. A. (1999) Biochem. Biophys. Res. Commun. 260, 273-279], deacetylate histones [Landry, J., Sutton, A., Tafrov, S. T., Heller, R. C., Stebbins, J., Pillus, L. & Sternglanz, R. (2000) Proc. Natl. Acad. Sci. USA 97, 5807-5811; Smith, J. S., Brachmann, C. B., Celic, I., Kenna, M. A., Muhammad, S., Starai, V. J., Avalos, J. L., Escalante-Semerena, J. C., Grubmeyer, C., Wolberger, C. & Boeke, J. D. (2000) Proc. Natl. Acad. Sci. USA 97, 6658-6663], or both [Imai, S., Armstrong, C. M., Kaeberlein, M. & Guarente, L. (2000) Nature (London) 403, 795-800]. Uncovering the true enzymatic function of SIR2 is critical to the basic understanding of its cellular function. Therefore, we set out to authenticate the reaction products and to determine the intrinsic catalytic mechanism. We provide direct evidence that the efficient histone/protein deacetylase reaction is tightly coupled to the formation of a previously unidentified acetyl-ADP-ribose product (1-O-acetyl-ADP ribose). One molecule of NAD+and one molecule of acetyl-lysine are readily catalyzed to one molecule of deacetylated lysine, nicotinamide, and 1-O-acetyl-ADP-ribose. A unique reaction mechanism involving the attack of enzyme-bound acetate or the direct attack of acetyl-lysine on an oxocarbenium ADP-ribose intermediate is proposed. We suggest that the reported histone/protein ADP-ribosyltransferase activity is a low-efficiency side reaction that can be explained through the partial uncoupling of the intrinsic deacetylation and acetate transfer to ADP-ribose.