An ATP-sensitive phosphoketolase regulates carbon fixation in cyanobacteria
Creators: name: Lu, Kuan-Jen
name: Chang, Chiung-Wen
name: Wang, Chun-Hsiung
name: Y-H Chen, Frederic
name: Y. Huang, Irene
name: Huang, Pin-Hsuan
name: Yang, Cheng-Han
name: Wu, Hsiang-Yi
name: Wu, Wen-Jin
name: Hsu, Kai-Cheng
name: Ho, Meng-Chiao
name: Tsai, Ming-Daw
Publisher: name: figshare
Year: 2023
Subjects: Cell metabolism
Structural biology (incl. macromolecular modelling)

description: This study is published in Nature metabolism 2023 in title "An ATP-sensitive phosphoketolase regulates carbon fixation in cyanobacteria".We discovered a CBB brake mechanism by a phosphoketolase in cyanobacterium <em>Synechococcus elongatus</em> PCC7942 (<em>Se</em>XPK), under low ATP conditions such as light to dark transitions. <em>Se</em>XPK is inhibited by high level of ATP (~1mM), as its kinetics data shown in <strong>Fig1</strong> and <strong>ED_Fig 1, </strong> When ATP drops under the transition from light to dark, the XPK deletion mutant continues to fix carbon for mintues, while the WT strain reduces carbon fixation immediately <strong>(Fig. 2)</strong>. Isotopic NaH<sup>13</sup>CO<sub>3</sub> feeding experiments showed that the XPK deletion strain fixed more carbon to synthesize hexose phosphates, typically glucose-6-phosphate, glucose-1-phosphate, and fructose-6-phosphate <strong>(Fig. 3)</strong> under transitions from light to dark. This data suggesting that XPK regulates carbon fixation brake by removing the rubisco substrate precursors of RuBP in CBB pathway. We also found that ATP levels of the cell cultures were reduced when cell cultures at high optical densities <strong>(Fig. 4 a)</strong>. In this condition, the carbon incorporation rate is increased by deletion of XPK <strong>(Fig. 4 b-e)</strong> and the sucrose is synthesized then excreted out of cells into culture medium <strong>(Fig. 4 g)</strong>. The biomass and protein levels were not changed by deletion of <em>Se</em>XPK, while less glycogen was found in the deletion strain <strong>(ED_Fig. 2)</strong>. The increase of carbon fixation by deletion of <em>Se</em>XPK is mainly resulted in sucrose production <strong>(Fig 4. h)</strong>. However, deletion of <em>Se</em>XPK does not influence carbon release in dark <strong>(Fig. 4 f)</strong>, photosynthesis, and dark respiration <strong>(Suppl table. 2)</strong>. We observed the growth retardation of the XPK deletion strain under high frequency light/dark cylces by imaging their autofluoresence increases in four days <strong>(Fig. 5)</strong>. We proposed mechanism schemes showing the regulatable role of SeXPK in carbon fixation (<strong>Fig. 8 and ED_Fig10).</strong> The RNA-seq data <strong>(ED_Fig3_RNAseq_TPM)</strong> of the WT and the XPK deletion mutant is deposited in NCBI GEO DataSets, and its accession number is GSE227397. The cryoEM structure of SeXPK with unique ATP binding mode is discovered, and the original maps have been deposited in the Protein Data Bank (PDB) and the Electron Microscopy Data Bank (EMDB) with the accession codes listed in Supplementary Table 3 in the manuscript. The <strong>PDB validation files </strong>as the zip file for <em>Se</em>XPK and <em>Bl</em>XPK structures and the protein data bank search <strong>(source data file I)</strong> are provided here. The blast result <strong>(source data file II)</strong> showed the unique ATP binding mode of <em>Se</em>XPK not only presenting in cyanobacteria but also many species.