Andrey Nikiforov

Pathways and Subcellular Compartmentation of NAD Biosynthesis in Human Cells FROM ENTRY OF EXTRACELLULAR PRECURSORS TO MITOCHONDRIAL NAD GENERATION

NAD is a vital redox carrier, and its degradation is a key element of important regulatory pathways. NAD-mediated functions are compartmentalized and have to be fueled by specific biosynthetic routes. However, little is known about the different pathways, their subcellular distribution, and regulation in human cells. In particular, the route(s) to generate mitochondrial NAD, the largest subcellular pool, is still unknown. To visualize organellar NAD changes in cells, we targeted poly(ADP-ribose) polymerase activity into the mitochondrial matrix. This activity synthesized immunodetectable poly(ADP-ribose) depending on mitochondrial NAD availability. Based on this novel detector system, detailed subcellular enzyme localizations, and pharmacological inhibitors, we identified extracellular NAD precursors, their cytosolic conversions, and the pathway of mitochondrial NAD generation. Our results demonstrate that, besides nicotinamide and nicotinic acid, only the corresponding nucleosides readily enter the cells. Nucleotides (e.g. NAD and NMN) undergo extracellular degradation resulting in the formation of permeable precursors. These precursors can all be converted to cytosolic and mitochondrial NAD. For mitochondrial NAD synthesis, precursors are converted to NMN in the cytosol. When taken up into the organelles, NMN (together with ATP) serves as substrate of NMNAT3 to form NAD. NMNAT3 was conclusively localized to the mitochondrial matrix and is the only known enzyme of NAD synthesis residing within these organelles. We thus present a comprehensive dissection of mammalian NAD biosynthesis, the groundwork to understand regulation of NAD-mediated processes, and the organismal homeostasis of this fundamental molecule.

The human NAD metabolome: Functions, metabolism and compartmentalization

Abstract The metabolism of NAD has emerged as a key regulator of cellular and organismal homeostasis. Being a major component of both bioenergetic and signaling pathways, the molecule is ideally suited to regulate metabolism and major cellular events. In humans, NAD is synthesized from vitamin B3 precursors, most prominently from nicotinamide, which is the degradation product of all NAD-dependent signaling reactions. The scope of NAD-mediated regulatory processes is wide including enzyme regulation, control of gene expression and health span, DNA repair, cell cycle regulation and calcium signaling. In these processes, nicotinamide is cleaved from NAD+ and the remaining ADP-ribosyl moiety used to modify proteins (deacetylation by sirtuins or ADP-ribosylation) or to generate calcium-mobilizing agents such as cyclic ADP-ribose. This review will also emphasize the role of the intermediates in the NAD metabolome, their intra- and extra-cellular conversions and potential contributions to subcellular compartmentalization of NAD pools.

Proteomic analysis of the 20S proteasome (PSMA3)-interacting proteins reveals a functional link between the proteasome and mRNA metabolism

The 26S proteasome is a large multi-subunit protein complex that exerts specific degradation of proteins in the cell. The 26S proteasome consists of the 20S proteolytic particle and the 19S regulator. In order to be targeted for proteasomal degradation most of the proteins must undergo the post-translational modification of poly-ubiquitination. However, a number of proteins can also be degraded by the proteasome via a ubiquitin-independent pathway. Such degradation is exercised largely through the binding of substrate proteins to the PSMA3 (alpha 7) subunit of the 20S complex. However, a systematic analysis of proteins interacting with PSMA3 has not yet been carried out. In this report, we describe the identification of proteins associated with PSMA3 both in the cytoplasm and nucleus. A combination of two-dimensional gel electrophoresis (2D-GE) and tandem mass-spectrometry revealed a large number of PSMA3-bound proteins that are involved in various aspects of mRNA metabolism, including splicing. In vitro biochemical studies confirmed the interactions between PSMA3 and splicing factors. Moreover, we show that 20S proteasome is involved in the regulation of splicing in vitro of SMN2 (survival motor neuron 2) gene, whose product controls apoptosis of neurons.

Generation, Release, and Uptake of the NAD Precursor Nicotinic Acid Riboside by Human Cells.

Background: Nicotinamide riboside (NR) and nicotinic acid riboside (NAR) can serve as precursors of NAD in human cells. Results: Human cells generate and release NR and NAR. Conclusion: NR and NAR are authentic intermediates of human NAD metabolism. Significance: Different cell populations might support each others NAD pools by providing ribosides as NAD precursors. NAD is essential for cellular metabolism and has a key role in various signaling pathways in human cells. To ensure proper control of vital reactions, NAD must be permanently resynthesized. Nicotinamide and nicotinic acid as well as nicotinamide riboside (NR) and nicotinic acid riboside (NAR) are the major precursors for NAD biosynthesis in humans. In this study, we explored whether the ribosides NR and NAR can be generated in human cells. We demonstrate that purified, recombinant human cytosolic 5′-nucleotidases (5′-NTs) CN-II and CN-III, but not CN-IA, can dephosphorylate the mononucleotides nicotinamide mononucleotide and nicotinic acid mononucleotide (NAMN) and thus catalyze NR and NAR formation in vitro. Similar to their counterpart from yeast, Sdt1, the human 5′-NTs require high (millimolar) concentrations of nicotinamide mononucleotide or NAMN for efficient catalysis. Overexpression of FLAG-tagged CN-II and CN-III in HEK293 and HepG2 cells resulted in the formation and release of NAR. However, NAR accumulation in the culture medium of these cells was only detectable under conditions that led to increased NAMN production from nicotinic acid. The amount of NAR released from cells engineered for increased NAMN production was sufficient to maintain viability of surrounding cells unable to use any other NAD precursor. Moreover, we found that untransfected HeLa cells produce and release sufficient amounts of NAR and NR under normal culture conditions. Collectively, our results indicate that cytosolic 5′-NTs participate in the conversion of NAD precursors and establish NR and NAR as integral constituents of human NAD metabolism. In addition, they point to the possibility that different cell types might facilitate each others NAD supply by providing alternative precursors.

Subcellular Distribution of NAD+ between Cytosol and Mitochondria Determines the Metabolic Profile of Human Cells.

Background: Maintaining the mitochondrial NAD+ pool is important, whereas its generation in mammalian cells is not understood. Results: A plant transporter expressed in human cells increases mitochondrial NAD+ but shifts metabolism from respiration to glycolysis. Conclusion: In human cells, NAD+ is synthesized in mitochondria rather than imported from the cytosol. Significance: Separation of subcellular NAD+ pools may be critical for metabolism in mammalian cells. The mitochondrial NAD pool is particularly important for the maintenance of vital cellular functions. Although at least in some fungi and plants, mitochondrial NAD is imported from the cytosol by carrier proteins, in mammals, the mechanism of how this organellar pool is generated has remained obscure. A transporter mediating NAD import into mammalian mitochondria has not been identified. In contrast, human recombinant NMNAT3 localizes to the mitochondrial matrix and is able to catalyze NAD+ biosynthesis in vitro. However, whether the endogenous NMNAT3 protein is functionally effective at generating NAD+ in mitochondria of intact human cells still remains to be demonstrated. To modulate mitochondrial NAD+ content, we have expressed plant and yeast mitochondrial NAD+ carriers in human cells and observed a profound increase in mitochondrial NAD+. None of the closest human homologs of these carriers had any detectable effect on mitochondrial NAD+ content. Surprisingly, constitutive redistribution of NAD+ from the cytosol to the mitochondria by stable expression of the Arabidopsis thaliana mitochondrial NAD+ transporter NDT2 in HEK293 cells resulted in dramatic growth retardation and a metabolic shift from oxidative phosphorylation to glycolysis, despite the elevated mitochondrial NAD+ levels. These results suggest that a mitochondrial NAD+ transporter, similar to the known one from A. thaliana, is likely absent and could even be harmful in human cells. We provide further support for the alternative possibility, namely intramitochondrial NAD+ synthesis, by demonstrating the presence of endogenous NMNAT3 in the mitochondria of human cells.

Reduced extractability of the XPA DNA repair protein in ultraviolet light-irradiated mammalian cells

The XPA protein is essential for both of the known modes of nucleotide excision repair (NER) in human cells: transcription‐coupled repair (TCR) and global genome repair (GGR). In TCR, this protein is thought to be recruited to lesion sites in DNA at which RNA polymerase II is blocked and in GGR, by direct recognition of damages by repair protein complex containing XPC/HR23B or DNA damage‐binding protein. However, details of the recruitment of the XPA protein in vivo are unknown. It was shown earlier that a portion of another NER protein, PCNA, which is completely extractable from non‐S‐phase mammalian nuclei, becomes insoluble after ultraviolet (UV) light irradiation and cannot be extracted by methanol or buffer containing Triton X‐100. In the present study, we have found that UV light irradiation of human or Chinese hamster cells leads to decrease of extractability of the XPA protein by Triton X‐100. Maximal insolubilization of the XPA protein is observed 1–4 h after irradiation but it is not detectable by 22 h. This effect is dose‐dependent for UV light from 2.5 to 15 J/m2 and is unaffected by the pre‐treatment of cells with sodium butyrate, an inhibitor of histone deacetylation. The UV light‐induced insolubilization of the XPA protein was also observed in two lines of Cockayne syndrome complementation group A cells, indicating that the effect is not dependent upon TCR. The results are discussed in relation to possible mechanisms of NER.

Polyclonal Antibodies Against Human Proteasome Subunits PSMA3, PSMA5, and PSMB5

A proteasome is a multi-subunit protein complex, which plays a central role in ubiquitin-dependent protein degradation in all eukaryotic cells. The 26S proteasome is composed of a catalytic 20S core complex and one or two 19S regulatory complexes. The 20S core complex forms a cylinder consisting of four stacked rings of seven α (PSMA1-7) or β (PSMB1-7) subunits. Target proteins are degraded in the cavity of the 20S complex due to proteolytic activities of three β subunits having catalytic sites located on the inner surface of the cylinder. The aim of this study was the generation of polyclonal antibodies against human proteasome subunits PSMA3, PSMA5, and PSMB5 and characterization of their experimental applications. To construct GST-fusion proteins, DNA sequences encoding PSMA3, PSMA5, and PSMB5 were cloned into prokaryotic expression vectors pGEX-5X-1 or pGEX-4T-3. Recombinant proteins GST-PSMA3, GST-PSMA5, and GST-PSMB5 were highly expressed in E. coli BL21 (DE3) cells, purified by glutathione-affinity chromatography and further used for rabbit immunization. The activity and specificity of the obtained antibody-containing sera were evaluated using Western blot analysis and immunoprecipitation. We have shown by Western blot analysis that our anti-PSMA3, anti-PSMA5, and anti-PSMB5 antibodies recognized both recombinant and endogenous proteins from different human cell lines. We have also shown that anti-PSMA3 and anti-PSMA5 sera were able to recognize and immunoprecipitate native forms of both endogenous and overexpressed FLAG-tagged proteins PSMA3 and PSMA5, respectively. Thus, the antibodies generated against PSMA3, PSMA5, and PSMB5 can be used in various experimental applications, including the evaluation of cellular levels of proteasome subunits in cell extracts and affinity purification of the endogenous and/or overexpressed proteasome subunits, which facilitates subsequent analysis of their post-translational modifications as well as protein-protein interactions in vivo.

STAUROSPORINE-SENSITIVE PROTEIN PHOSPHORYLATION IS REQUIRED FOR POSTREPLICATION DNA REPAIR IN HUMAN CELLS

DNA repair is an important factor of stability of pro‐ and eukaryotic genomes which plays a central role in mutagenesis and carcinogenesis. Genetic control of nucleotide excision repair (NER) in mammalian cells is well studied, but little is known about molecular mechanisms of postreplication repair (PRR) which allows bypass of base lesions in template strands after DNA replication. In Saccharomyces cerevisiae PRR is controlled by the RAD6/RAD18 pathway which involves POL30 gene encoding proliferating cell nuclear antigen (PCNA), and in human cells PCNA is known to be closely associated with the newly replicated chromatin where PRR probably takes place. In UV‐irradiated human cells distinct PCNA foci may be detected in some cells which accumulate phosphorylated breast cancer susceptibility protein BRCA1 and another protein BARD1. Human PCNA is also known to be phosphorylated after UV‐irradiation. In this study we found that the known inhibitor of protein kinases staurosporine supresses PRR in NER‐deficient cells which is consistent with the view that BRCA1 and PCNA are required for PRR. We also have shown that the distinct PCNA foci in UV‐irradiated NER‐deficient cells are actually associated with the newly replicated chromatin. Since RAD18 protein is not essential for normal DNA replication and directly controls PRR in yeast, we analysed whether this protein as well as its human homologs (HR18A and HR18B) have common domains with BRCA1 and BARD1. It is found that HR18A has a subregion of homology to BARD1 and HR18A‐to BRCA1. Taken together the results indicate that BRCA1 and BARD1 may be involved in PRR in human cells.

Immunoaffinity purification of the functional 20S proteasome from human cells via transient overexpression of specific proteasome subunits.

The proteasome is a multi-subunit proteolytic complex that plays a central role in protein degradation in all eukaryotic cells. It regulates many vital cellular processes therefore its dysfunction can lead to various pathologies including cancer and neurodegeneration. Isolation of enzymatically active proteasomes is a key step to the successful study of the proteasome regulation and functions. Here we describe a simple and efficient protocol for immunoaffinity purification of the functional 20S proteasomes from human HEK 293T cells after transient overexpression of specific proteasome subunits tagged with 3xFLAG. To construct 3xFLAG-fusion proteins, DNA sequences encoding the 20S proteasome subunits PSMB5, PSMA5, and PSMA3 were cloned into mammalian expression vector pIRES-hrGFP-1a. The corresponding recombinant proteins PSMB5-3xFLAG, PSMA5-3xFLAG, or PSMA3-3xFLAG were transiently overexpressed in human HEK 293T cells and were shown to be partially incorporated into the intact proteasome complexes. 20S proteasomes were immunoprecipitated from HEK 293T cell extracts under mild conditions using antibodies against FLAG peptide. Isolation of highly purified 20S proteasomes were confirmed by SDS-PAGE and Western blotting using antibodies against different proteasome subunits. Affinity purified 20S proteasomes were shown to possess chymotrypsin- and trypsin-like peptidase activities confirming their functionality. This simple single-step affinity method of the 20S proteasome purification can be instrumental to subsequent functional studies of proteasomes in human cells.

Compartment-Specific Poly-ADP-Ribose Formation as a Biosensor for Subcellular NAD Pools

Nicotinamide adenine dinucleotide (NAD) is vital to many cellular processes and is distributed between distinct subcellular pools in the compartmentalized eukaryotic cell. The detection and relative quantification of these individual pools is difficult because of the methods usually applied, which require cell disruption and fractionation.Here, we describe an immunochemical method to visualize and relatively quantify subcellular NAD+ pools, which relies on the NAD+-consuming activity of poly-ADP-ribose polymerase 1 (PARP1). We demonstrate that this system can be readily applied to detect changes in the mitochondrial, Golgi, endoplasmic reticulum, and peroxisomal NAD+ pools.