Pyruvate Kinase, a Metabolic Sensor Powering Glycolysis, Drives the Metabolic Control of DNA Replication

Overview

Journal BMC Biol

Publisher Biomed Central

Specialty Biology

Date 2022 Apr 14

PMID 35418203

Authors

Steff Horemans

Matthaios Pitoulias

Alexandria Holland

Emilie Pateau

Christophe Lechaplais

Dariy Ekaterina

Alain Perret

Panos Soultanas

Laurent Janniere

Affiliations

Soon will be listed here.

Abstract

Background: In all living organisms, DNA replication is exquisitely regulated in a wide range of growth conditions to achieve timely and accurate genome duplication prior to cell division. Failures in this regulation cause DNA damage with potentially disastrous consequences for cell viability and human health, including cancer. To cope with these threats, cells tightly control replication initiation using well-known mechanisms. They also couple DNA synthesis to nutrient richness and growth rate through a poorly understood process thought to involve central carbon metabolism. One such process may involve the cross-species conserved pyruvate kinase (PykA) which catalyzes the last reaction of glycolysis. Here we have investigated the role of PykA in regulating DNA replication in the model system Bacillus subtilis.

Results: On analysing mutants of the catalytic (Cat) and C-terminal (PEPut) domains of B. subtilis PykA we found replication phenotypes in conditions where PykA is dispensable for growth. These phenotypes are independent from the effect of mutations on PykA catalytic activity and are not associated with significant changes in the metabolome. PEPut operates as a nutrient-dependent inhibitor of initiation while Cat acts as a stimulator of replication fork speed. Disruption of either PEPut or Cat replication function dramatically impacted the cell cycle and replication timing even in cells fully proficient in known replication control functions. In vitro, PykA modulates activities of enzymes essential for replication initiation and elongation via functional interactions. Additional experiments showed that PEPut regulates PykA activity and that Cat and PEPut determinants important for PykA catalytic activity regulation are also important for PykA-driven replication functions.

Conclusions: We infer from our findings that PykA typifies a new family of cross-species replication control regulators that drive the metabolic control of replication through a mechanism involving regulatory determinants of PykA catalytic activity. As disruption of PykA replication functions causes dramatic replication defects, we suggest that dysfunctions in this new family of universal replication regulators may pave the path to genetic instability and carcinogenesis.

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References

Noirot-Gros M, Dervyn E, Wu L, Mervelet P, Errington J, Ehrlich S . An expanded view of bacterial DNA replication. Proc Natl Acad Sci U S A. 2002; 99(12):8342-7. PMC: 123069. DOI: 10.1073/pnas.122040799. View

Tymecka-Mulik J, Boss L, Maciag-Dorszynska M, Matias Rodrigues J, Gaffke L, Wosinski A . Suppression of the Escherichia coli dnaA46 mutation by changes in the activities of the pyruvate-acetate node links DNA replication regulation to central carbon metabolism. PLoS One. 2017; 12(4):e0176050. PMC: 5407757. DOI: 10.1371/journal.pone.0176050. View

Ewald J, Kuehne A, Zamboni N, Skotheim J . The Yeast Cyclin-Dependent Kinase Routes Carbon Fluxes to Fuel Cell Cycle Progression. Mol Cell. 2016; 62(4):532-45. PMC: 4875507. DOI: 10.1016/j.molcel.2016.02.017. View

Jameson K, Wilkinson A . Control of Initiation of DNA Replication in Bacillus subtilis and Escherichia coli. Genes (Basel). 2017; 8(1). PMC: 5295017. DOI: 10.3390/genes8010022. View

Maya-Mendoza A, Moudry P, Merchut-Maya J, Lee M, Strauss R, Bartek J . High speed of fork progression induces DNA replication stress and genomic instability. Nature. 2018; 559(7713):279-284. DOI: 10.1038/s41586-018-0261-5. View

Lu M, Campbell J, Boye E, Kleckner N . SeqA: a negative modulator of replication initiation in E. coli. Cell. 1994; 77(3):413-26. DOI: 10.1016/0092-8674(94)90156-2. View

Seror S, Casaregola S, Vannier F, Zouari N, Dahl M, Boye E . A mutant cysteinyl-tRNA synthetase affecting timing of chromosomal replication initiation in B. subtilis and conferring resistance to a protein kinase C inhibitor. EMBO J. 1994; 13(10):2472-80. PMC: 395113. DOI: 10.1002/j.1460-2075.1994.tb06532.x. View

Reiland S, Messerli G, Baerenfaller K, Gerrits B, Endler A, Grossmann J . Large-scale Arabidopsis phosphoproteome profiling reveals novel chloroplast kinase substrates and phosphorylation networks. Plant Physiol. 2009; 150(2):889-903. PMC: 2689975. DOI: 10.1104/pp.109.138677. View

Mathews C . Deoxyribonucleotide metabolism, mutagenesis and cancer. Nat Rev Cancer. 2015; 15(9):528-39. DOI: 10.1038/nrc3981. View

10.

Berge M, Pezzatti J, Gonzalez-Ruiz V, Degeorges L, Mottet-Osman G, Rudaz S . Bacterial cell cycle control by citrate synthase independent of enzymatic activity. Elife. 2020; 9. PMC: 7083601. DOI: 10.7554/eLife.52272. View

11.

Yao N, Georgescu R, Finkelstein J, ODonnell M . Single-molecule analysis reveals that the lagging strand increases replisome processivity but slows replication fork progression. Proc Natl Acad Sci U S A. 2009; 106(32):13236-41. PMC: 2726342. DOI: 10.1073/pnas.0906157106. View

12.

Schormann N, Hayden K, Lee P, Banerjee S, Chattopadhyay D . An overview of structure, function, and regulation of pyruvate kinases. Protein Sci. 2019; 28(10):1771-1784. PMC: 6739817. DOI: 10.1002/pro.3691. View

13.

Paschalis V, Le Chatelier E, Green M, Nouri H, Kepes F, Soultanas P . Interactions of the DnaE polymerase with replisomal proteins modulate its activity and fidelity. Open Biol. 2017; 7(9). PMC: 5627055. DOI: 10.1098/rsob.170146. View

14.

Washington T, Smith J, Grossman A . Genetic networks controlled by the bacterial replication initiator and transcription factor DnaA in Bacillus subtilis. Mol Microbiol. 2017; 106(1):109-128. PMC: 5607098. DOI: 10.1111/mmi.13755. View

15.

Burnetti A, Aydin M, Buchler N . Cell cycle Start is coupled to entry into the yeast metabolic cycle across diverse strains and growth rates. Mol Biol Cell. 2015; 27(1):64-74. PMC: 4694762. DOI: 10.1091/mbc.E15-07-0454. View

16.

Hu C, Tien S, Hsieh P, Jeng Y, Chang M, Chang Y . High Glucose Triggers Nucleotide Imbalance through O-GlcNAcylation of Key Enzymes and Induces KRAS Mutation in Pancreatic Cells. Cell Metab. 2019; 29(6):1334-1349.e10. DOI: 10.1016/j.cmet.2019.02.005. View

17.

Thomas M, Stuani L, Darii E, Lechaplais C, Pateau E, Tabet J . De novo structure determination of 3-((3-aminopropyl)amino)-4-hydroxybenzoic acid, a novel and abundant metabolite in Acinetobacter baylyi ADP1. Metabolomics. 2019; 15(3):45. DOI: 10.1007/s11306-019-1508-3. View

18.

Bollenbach T, Mesecar A, Nowak T . Role of lysine 240 in the mechanism of yeast pyruvate kinase catalysis. Biochemistry. 1999; 38(28):9137-45. DOI: 10.1021/bi990690n. View

19.

Chambers M, MacLean B, Burke R, Amodei D, Ruderman D, Neumann S . A cross-platform toolkit for mass spectrometry and proteomics. Nat Biotechnol. 2012; 30(10):918-20. PMC: 3471674. DOI: 10.1038/nbt.2377. View

20.

Oskam L, Hillenga D, Venema G, Bron S . The large Bacillus plasmid pTB19 contains two integrated rolling-circle plasmids carrying mobilization functions. Plasmid. 1991; 26(1):30-9. DOI: 10.1016/0147-619x(91)90034-t. View