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A journey into the regulatory secrets of the de novo purine nucleotide biosynthesis - PubMed

  • ️Mon Jan 01 2024

Review

A journey into the regulatory secrets of the de novo purine nucleotide biosynthesis

Nour Ayoub et al. Front Pharmacol. 2024.

Abstract

De novo purine nucleotide biosynthesis (DNPNB) consists of sequential reactions that are majorly conserved in living organisms. Several regulation events take place to maintain physiological concentrations of adenylate and guanylate nucleotides in cells and to fine-tune the production of purine nucleotides in response to changing cellular demands. Recent years have seen a renewed interest in the DNPNB enzymes, with some being highlighted as promising targets for therapeutic molecules. Herein, a review of two newly revealed modes of regulation of the DNPNB pathway has been carried out: i) the unprecedent allosteric regulation of one of the limiting enzymes of the pathway named inosine 5'-monophosphate dehydrogenase (IMPDH), and ii) the supramolecular assembly of DNPNB enzymes. Moreover, recent advances that revealed the therapeutic potential of DNPNB enzymes in bacteria could open the road for the pharmacological development of novel antibiotics.

Keywords: IMP dehydrogenase; allostery; antibacterial agents; chemical compounds; enzyme regulation; nucleotide biosynthesis; protein structure-function relationship; protein-protein interactions.

Copyright © 2024 Ayoub, Gedeon and Munier-Lehmann.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

FIGURE 1
FIGURE 1

Schematic representation of the de novo and salvage pathways of purine and pyrimidine ribonucleotides. Each arrow represents one chemical step. This figure is not exhaustive.

FIGURE 2
FIGURE 2

DNPNB pathway. Representation of the sequential conversion of PRPP into AMP and GMP via the de novo biosynthetic pathway of purine nucleotides. The steps are labeled with specific colors and numbered, with a corresponding list of enzymes involved in each step provided for both bacteria and vertebrates (see Table 1). In vertebrates, six enzymes are responsible for converting PRPP to IMP, which is then further processed into GMP or AMP by several additional reactions. Prokaryotes, on the other hand, require fourteen enzymes to catalyze the chemical steps. The structure of each E. coli enzyme is illustrated. Resolved structures of E. coli enzymes have the following PDB accession numbers: 1ECB (PurF), 1GSO (PurD), 1CDE (PurN), 1KJ8 (PurT); 1CLI (PurM), 1D7A (PurE), 1B6S (PurK), 2GQS (PurC), 1PTR (PurB), 1GPM (GuaA), 1ADE (PurA). For other E. coli enzymes to which no structure was resolved, the ortholog structures are shown with the following PDB accession numbers and percentage of sequence identities: 6JTA (Salmonella typhimurium PurL, 94% identity), 4A1O (Mycobacterium tuberculosis PurH, 43% identity), and 4DQW (Pseudomonas aeruginosa IMPDH, 66% identity).

FIGURE 3
FIGURE 3

Schematic representation of the structural domains of enzymes involved in steps 2 (GARS, PurD), 3 (GART, PurN), 3'(PurT), 5 (AIRS, PurM), 6 (CAIRS, PurE), 6’ (PurK), 7 (SAICARS, PurC), 9 (AICART, PurH) and 10 (IMPC, PurH) in vertebrates and bacteria taking as representatives human and E. coli enzymes.

FIGURE 4
FIGURE 4

Organization of the genes encoding the enzymes of the de novo pathway, and their mode of transcriptional regulation by PurR in E. coli (A), B. subtilis (B) and L. lactis (C). Data are extracted from the BioCyc database (Caspi et al., 2020). In each panel, coding regions are shown by boxes with the same color code as in Figure 2. Horizontal arrows show the transcription direction from the promoters regulated by PurR and the +1 represents the first nucleotide transcribed. Of note, the PurR found in E. coli is non-homologous to the ones present in B. subtilis and L. lactis. Above the schematic diagram are detailed the regulatory elements on purMN operon as an example for E. coli and L. lactis and on the single pur operon for B. subtilis. (A) PurR (brown) interacts through a DNA binding sequence in the different pur operons or single genes and blocks the interaction of the RNA polymerase (RNA pol in black) with the TATA box, thus inhibiting the transcription. Hypoxanthine and guanine (mauve) are corepressors. (B) The interaction of (p)ppGpp (pink) with PurR (light cobalt blue) favors PurR binding to a DNA binding site composed of two boxes PurBox1 and PurBox2 upstream of the pur operon and inhibit the transcription of DNA. Conformational changes in PurR that occur upon PRPP (orange) binding inhibits PurR-DNA interaction, that results in the activation of DNA transcription. (C) The PurR (light cobalt blue) is in continuous interaction with DNA but only becomes activated after binding of PRPP (orange) on its allosteric site, which induces the recruitment of RNA polymerase (RNA pol in black) that binds to the TATA box of the promoter.

FIGURE 5
FIGURE 5

Overview of the regulators of the PRPP synthetase and DNPNB enzymes from E. coli, apart from IMPDH (step 11) for which the regulation will be elaborated below (Section 3.2 and list of inhibitors and activators in Table 2). NXP corresponds to 5′-mono, di or triphosphate nucleotides. Inhibitors are in red, and the only activator (PRPP) is in green. Regulators marked with an asterisk (*) were also shown to be modulators for the human counterparts.

FIGURE 6
FIGURE 6

IMPDH structural overview. (A) Primary sequence as a schematic bar representation to position the Bateman domain (BD, green) composed of two CBS modules and the catalytic domain (CD, lavender). Important loops of the catalytic domain are colored as follows: catalytic loop in pink, finger loop in yellow, flap loop in orange and C-terminal loop in blue. (B) 3D structure of IMPDH monomer in ribbon representation, showing the Bateman domain and the catalytic domain with important loops (same color as in A). (C, D) Zoom on the Bateman domain of IMPDHpa (C; PDB 4DQW) and that of IMPDHag (D; PDB 4Z87) with two ATP molecules and three GDP molecules shown in sticks, respectively. (E) Summary diagram of the structural transitions at the level of the loops of the catalytic domain (same color code as in A) during catalysis. When loops are not ordered, they are represented as dashed lines.

FIGURE 7
FIGURE 7

Overview of the regulation of DNPNB enzyme clustering and purinosome assembly-disassembly under the control of regulatory proteins and signaling pathways. Each circle corresponds to one step of the DNPNB pathway: same color code and numbering as in Table 1. The green filaments represent microtubules. The figure was created with

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. AMPK, AMP-activated protein kinase; CK2, casein kinase 2; PDK1, 3-phosphoinositide-dependent kinase-1; PI3K, phosphatidylinositol 3-kinase; PI-2P, phosphatidylinositol (4,5)-bisphosphate; PI-3P, phosphatidylinositol (3,4,5)-trisphosphate; PKC, protein kinase C; S6K, p70 ribosomal S6 kinase.

FIGURE 8
FIGURE 8

Described protein-protein interactions within the purinosome (Deng et al., 2012; Zhao et al., 2015; Agarwal et al., 2020a; He et al., 2022). Solved 3D-structures of human enzymes (same acronym and color code as in Table 1) have the following PDB accession numbers: 7ALE (PAICS), 4FFX (ADSL), 1PKX (ATIC), 2V40 (hADSS2), 1JCN (hIMPDH1). TrifGART was modeled based on previous published structural data (Welin et al., 2010) and from structures of each of the individual three domains (2QK4 for GARS, 2V9Y for AIRS, 1RBY for GART). The human FGAMS structure was predicted with AlphaFold2 (Jumper et al., 2021). For PPAT, the ortholog from Arabidopsis thaliana (PDB 6LBP; 39% identity) is depicted.

FIGURE 9
FIGURE 9

Described protein-protein interactions between E. coli DNPNB enzymes (Gedeon et al., 2023b). Each enzyme (same acronym and color code as in Table 1) is represented by its 3D-structure (for the PDB accession numbers, see Figure 2).

FIGURE 10
FIGURE 10

Some human IMPDH inhibitors.

FIGURE 11
FIGURE 11

Novel chemical entities as potent bacterial IMPDH inhibitors. See text for references.

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References

    1. Agarwal S., Chakravarthi B. V. S. K., Behring M., Kim H.-G., Chandrashekar D. S., Gupta N., et al. (2020a). PAICS, a purine nucleotide metabolic enzyme, is involved in tumor growth and the metastasis of colorectal cancer. Cancers 12 (4), 772. 10.3390/cancers12040772 - DOI - PMC - PubMed
    1. Agarwal S., Chakravarthi B. V. S. K., Kim H.-G., Gupta N., Hale K., Balasubramanya S. A. H., et al. (2020b). PAICS, a de novo purine biosynthetic enzyme, is overexpressed in pancreatic cancer and is involved in its progression. Transl. Oncol. 13 (7), 100776. 10.1016/j.tranon.2020.100776 - DOI - PMC - PubMed
    1. Aiba A., Mizobuchi K. (1989). Nucleotide sequence analysis of genes purH and purD involved in the de novo purine nucleotide biosynthesis of Escherichia coli . J. Biol. Chem. 264 (35), 21239–21246. 10.1016/s0021-9258(19)30072-9 - DOI - PubMed
    1. Alexandre T., Lupan A., Helynck O., Vichier-Guerre S., Dugue L., Gelin M., et al. (2019). First-in-class allosteric inhibitors of bacterial IMPDHs. Eur. J. Med. Chem. 167, 124–132. 10.1016/j.ejmech.2019.01.064 - DOI - PubMed
    1. Alexandre T., Raynal B., Munier-Lehmann H. (2015). Two classes of bacterial IMPDHs according to their quaternary structures and catalytic properties. PLoS ONE 10 (2), e0116578. 10.1371/journal.pone.0116578 - DOI - PMC - PubMed

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The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This work was supported in part by the Centre National de la Recherche Scientifique (CNRS), the Institut National de la Santé Et de la Recherche Médicale (INSERM) and the Institut Pasteur.

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