Pyrophosphorylases and Phosphorylases in Biosynthetic Reactions

Kornberg, Arthur

doi:10.1002/9780470122631.ch5

Cited by 26 publications

(12 citation statements)

References 208 publications

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“…Inorganic pyrophosphate (PPi) was discovered in the 19 th century and, in 1941, was found to accumulate in rat livers; this was the first report on PPi accumulation in a biological system 1 . Later, Kornberg described the first PPi-producing biological reaction 2 and proposed that pyrophosphorylases acted in the direction of PPi production favoring the formation of biochemical compounds 3 . Further, it was suggested that inorganic pyrophosphatase (PPase)-mediated PPi hydrolysis rendered the above reactions practically irreversible 4 , a hypothesis that is now widely accepted.…”

Section: Introductionmentioning

confidence: 99%

Pyrophosphate inhibits gluconeogenesis by restricting UDP-glucose formation in vivo

Ferjani

Kawade

Asaoka

et al. 2018

Sci Rep

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Pyrophosphate (PPi) is produced by anabolic reactions and serves as an energy donor in the cytosol of plant cells; however, its accumulation to toxic levels disrupts several common biosynthetic pathways and is lethal. Before acquiring photosynthetic capacity, young seedlings must endure a short but critical heterotrophic period, during which they are nourished solely by sugar produced from seed reserves by the anabolic process of gluconeogenesis. Previously, we reported that excess PPi in H+-PPase-knockout fugu5 mutants of Arabidopsis thaliana severely compromised gluconeogenesis. However, the precise metabolic target of PPi inhibition in vivo remained elusive. Here, CE-TOF MS analyses of major metabolites characteristic of gluconeogenesis from seed lipids showed that the Glc6P;Fru6P level significantly increased and that Glc1P level was consistently somewhat higher in fugu5 compared to wild type. In contrast, the UDP-Glc level decreased significantly in the mutants. Importantly, specific removal of PPi in fugu5, and thus in AVP1pro:IPP1 transgenic lines, restored the Glc1P and the Glc6P;Fru6P levels, increased the UDP-Glc level ~2.0-fold, and subsequently increased sucrose synthesis. Given the reversible nature of the Glc1P/UDP-Glc reaction, our results indicate that UGP-Glc pyrophosphorylase is the major target when excess PPi exerts inhibitory effects in vivo. To validate our findings, we analyzed metabolite responses using a mathematical theory called structural sensitivity analysis (SSA), in which the responses of concentrations in reaction systems to perturbations in enzyme activity are determined from the structure of the network alone. A comparison of our experimental data with the results of pure structural theory predicted the existence of unknown reactions as the necessary condition for the above metabolic profiles, and confirmed the above results. Our data support the notion that H+-PPase plays a pivotal role in cytosolic PPi homeostasis in plant cells. We propose that the combination of metabolomics and SSA is powerful when seeking to identify and predict metabolic targets in living cells.

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Section: Introductionmentioning

confidence: 99%

Pyrophosphate inhibits gluconeogenesis by restricting UDP-glucose formation in vivo

Ferjani

Kawade

Asaoka

et al. 2018

Sci Rep

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“…In the 1950s, Kornberg and colleagues recognised that the hydrolysis of intracellular pyrophosphate was a major mechanism for driving biosynthetic reactions in the direction of synthesis [2]. Huge amounts of pyrophosphate are produced within cells daily, particularly during the generation of macromolecules such as proteins, nucleic acids, carbohydrates and lipids from their smaller precursors.…”

Section: Introductionmentioning

confidence: 99%

Pyrophosphate: a key inhibitor of mineralisation

Orriss

Arnett

Russell

2016

Current Opinion in Pharmacology

146

105

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“…That NDPs could support efficient polymerization stems from the precedent of polynucleotide phosphorylase (24), which releases P i as its reaction product. Unlike PNP, however, nucleotide polymerization with NTPs or dNTPs by RNAP or DNAP is not readily reversible because the pyrophosphate reaction product is rapidly cleaved by inorganic pyrophosphatase, which maintains a low micromolar level of intracellular pyrophosphate concentration (25). In contrast, NDP polymerization yields P i , whose concentration in the cell is high, about 0.01-0.1 M (26,27).…”

Section: Ndps Are Substrates For Nucleic Acid Polymerasesmentioning

confidence: 99%

Ribonucleoside-5′-diphosphates (NDPs) support RNA polymerase transcription, suggesting NDPs may have been substrates for primordial nucleic acid biosynthesis

Gottesman

Mustaev

2019

Journal of Biological Chemistry

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Edited by Patrick Sung A better understanding of the structural basis for the preferences of RNA and DNA polymerases for nucleoside-5-triphosphates (NTPs) could help define the catalytic mechanisms for nucleotidyl transfer during RNA and DNA synthesis and the origin of primordial nucleic acid biosynthesis. We show here that ribonucleoside-5-diphosphates (NDPs) can be utilized as substrates by RNA polymerase (RNAP). We found that NDP incorporation is template-specific and that noncognate NDPs are not incorporated. Compared with the natural RNAP substrates, NTPs, the K m of RNAP for NDPs was increased ϳ4-fold, whereas the V max was decreased ϳ200-fold. These properties could be accounted for by molecular modeling of NTP/RNAP co-crystal structures. This finding suggested that the terminal phosphate residue in NTP (not present in NDP) is important for positioning the nucleotide for nucleolytic attack in the nucleotidyl transfer reaction. Strikingly, a mutational substitution of the active-center ␤R1106 side chain involved in NTP positioning also strongly inhibited NDP-directed synthesis, even though this residue does not contact NDP. Substitutions in the structurally analogous side chain in RB69 DNA polymerase (Arg-482) and HIV reverse transcriptase (Lys-65) were previously observed to inhibit dNDP incorporation. The unexpected involvement of these residues suggests that they affect a step in catalysis common for nucleic acid polymerases. The substrate activity of NDPs with RNAP along with those reported for DNA polymerases reinforces the hypothesis that NDPs may have been used for nucleic acid biosynthesis by primordial enzymes, whose evolution then led to the use of the more complex triphosphate derivatives. cro ARTICLE

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Pyrophosphorylases and Phosphorylases in Biosynthetic Reactions

Cited by 26 publications

References 208 publications

Pyrophosphate inhibits gluconeogenesis by restricting UDP-glucose formation in vivo

Pyrophosphate inhibits gluconeogenesis by restricting UDP-glucose formation in vivo

Pyrophosphate: a key inhibitor of mineralisation

Ribonucleoside-5′-diphosphates (NDPs) support RNA polymerase transcription, suggesting NDPs may have been substrates for primordial nucleic acid biosynthesis

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