Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Phosphoketolase pathway contributes to carbon metabolism in cyanobacteria


Central carbon metabolism in cyanobacteria comprises the Calvin–Benson–Bassham (CBB) cycle, glycolysis, the pentose phosphate (PP) pathway and the tricarboxylic acid (TCA) cycle. Redundancy in this complex metabolic network renders the rational engineering of cyanobacterial metabolism for the generation of biomass, biofuels and chemicals a challenge. Here we report the presence of a functional phosphoketolase pathway, which splits xylulose-5-phosphate (or fructose-6-phosphate) to acetate precursor acetyl phosphate, in an engineered strain of the model cyanobacterium Synechocystis (ΔglgC/xylAB), in which glycogen synthesis is blocked, and xylose catabolism enabled through the introduction of xylose isomerase and xylulokinase. We show that this mutant strain is able to metabolise xylose to acetate on nitrogen starvation. To see whether acetate production in the mutant is linked to the activity of phosphoketolase, we disrupted a putative phosphoketolase gene (slr0453) in the ΔglgC/xylAB strain, and monitored metabolic flux using 13C labelling; acetate and 2-oxoglutarate production was reduced in the light. A metabolic flux analysis, based on isotopic data, suggests that the phosphoketolase pathway metabolises over 30% of the carbon consumed by ΔglgC/xylAB during photomixotrophic growth on xylose and CO2. Disruption of the putative phosphoketolase gene in wild-type Synechocystis also led to a deficiency in acetate production in the dark, indicative of a contribution of the phosphoketolase pathway to heterotrophic metabolism. We suggest that the phosphoketolase pathway, previously uncharacterized in photosynthetic organisms, confers flexibility in energy and carbon metabolism in cyanobacteria, and could be exploited to increase the efficiency of cyanobacterial carbon metabolism and photosynthetic productivity.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Rent or buy this article

Get just this article for as long as you need it


Prices may be subject to local taxes which are calculated during checkout

Figure 1: The engineered central carbon metabolism in the cyanobacterium Synechocystis.
Figure 2: Identification of acetate in cell-free ΔglgC/xylAB culture medium supplemented with xylose.
Figure 3: Production of organic acids by ΔglgC/xylAB/Δslr0453 (red columns) and ΔglgC/xylAB (white columns).
Figure 4: Acetate productivity in the presence or absence of Slr0453.
Figure 5: Simulation of fractional 13C-labelling of serine from [U-13C]- and [1-13C]xylose tracer experiments.


  1. McEwen, J. T., Machado, I. M. P., Connor, M. R. & Atsumi, S. Engineering Synechococcus elongatus PCC 7942 for continuous growth under diurnal conditions. Appl. Environ. Microbiol. 79, 1668–1675 (2013).

    Article  CAS  Google Scholar 

  2. Lee, T. C. et al. Engineered xylose utilization enhances bio-products productivity in the cyanobacterium Synechocystis sp. PCC 6803. Metab. Eng. 30, 179–189 (2015).

    Article  CAS  Google Scholar 

  3. Yan, C. L. & Xu, X. D. Bifunctional enzyme FBPase/SBPase is essential for photoautotrophic growth in cyanobacterium Synechocystis sp PCC 6803. Prog. Nat. Sci. 18, 149–153 (2008).

    Article  CAS  Google Scholar 

  4. Bricker, T. M. et al. The malic enzyme is required for optimal photoautotrophic growth of Synechocystis sp. strain PCC 6803 under continuous light but not under a diurnal light regimen. J. Bacteriol. 186, 8144–8148 (2004).

    Article  CAS  Google Scholar 

  5. Jansen, T. et al. Characterization of trophic changes and a functional oxidative pentose phosphate pathway in Synechocystis sp PCC 6803. Acta Physiol. Plant. 32, 511–518 (2010).

    Article  CAS  Google Scholar 

  6. Xiong, W., Brune, D. & Vermaas, W. F. J. The gamma-aminobutyric acid shunt contributes to closing the tricarboxylic acid cycle in Synechocystis sp PCC 6803. Mol. Microbiol. 93, 786–796 (2014).

    Article  CAS  Google Scholar 

  7. Gu, Z. L. et al. Role of duplicate genes in genetic robustness against null mutations. Nature 421, 63–66 (2003).

    Article  CAS  Google Scholar 

  8. Valverde, F. et al. Simultaneous occurrence of two different glyceraldehyde-3-phosphate dehydrogenases in heterocystous N2-fixing cyanobacteria. Biochem. Biophys. Res. Commun. 283, 356–363 (2001).

    Article  CAS  Google Scholar 

  9. Holtman, C. K. et al. High-throughput functional analysis of the Synechococcus elongatus PCC 7942 genome. DNA Res. 12, 103–115 (2005).

    Article  CAS  Google Scholar 

  10. Tyo, K. E., Jin, Y. S., Espinoza, F. A. & Stephanopoulos, G. Identification of gene disruptions for increased poly-3-hydroxybutyrate accumulation in Synechocystis PCC 6803. Biotechnol. Prog. 25, 1236–1243 (2009).

    Article  CAS  Google Scholar 

  11. Yang, C., Hua, Q. & Shimizu, K. Metabolic flux analysis in Synechocystis using isotope distribution from 13C-labeled glucose. Metab. Eng. 4, 202–216 (2002).

    Article  CAS  Google Scholar 

  12. Young, J. D., Shastri, A. A., Stephanopoulos, G. & Morgan, J. A. Mapping photoautotrophic metabolism with isotopically nonstationary 13C flux analysis. Metab. Eng. 14, 185–185 (2012).

    Article  CAS  Google Scholar 

  13. Xiong, W. et al. The plasticity of cyanobacterial metabolism supports direct CO2 conversion to ethylene. Nature Plants 1, 15053 (2015).

    Article  CAS  Google Scholar 

  14. Carrieri, D., Paddock, T., Maness, P. C., Seibert, M. & Yu, J. P. Photo-catalytic conversion of carbon dioxide to organic acids by a recombinant cyanobacterium incapable of glycogen storage. Energ. Environ. Sci. 5, 9457–9461 (2012).

    Article  CAS  Google Scholar 

  15. Grundel, M., Scheunemann, R., Lockau, W. & Zilliges, Y. Impaired glycogen synthesis causes metabolic overflow reactions and affects stress responses in the cyanobacterium Synechocystis sp PCC 6803. Microbiology 158, 3032–3043 (2012).

    Article  Google Scholar 

  16. McNeely, K. et al. Synechococcus sp. strain PCC 7002 nifJ mutant lacking pyruvate:ferredoxin oxidoreductase. Appl. Environ. Microbiol. 77, 2435–2444 (2011).

    Article  CAS  Google Scholar 

  17. Zhou, J., Zhang, H. F., Zhang, Y. P., Li, Y. & Ma, Y. H. Designing and creating a modularized synthetic pathway in cyanobacterium Synechocystis enables production of acetone from carbon dioxide. Metab. Eng. 14, 394–400 (2012).

    Article  CAS  Google Scholar 

  18. Fandi, K. G., Ghazali, H. M., Yazid, A. M. & Raha, A. R. Purification and N-terminal amino acid sequence of fructose-6-phosphate phosphoketolase from Bifidobacterium longum BB536. Lett. Appl. Microbiol. 32, 235–239 (2001).

    Article  CAS  Google Scholar 

  19. Meile, L., Rohr, L. M., Geissman, T. A., Herensperger, M. & Teuber, M. Characterization of the D-xylulose 5-phosphate/D-fructose 6-phosphate phosphoketolase gene (xfp) from Bifidobacterium lactis. J. Bacteriol. 183, 2929–2936 (2001).

    Article  CAS  Google Scholar 

  20. Amaya-Delgado, L., Hidalgo-Lara, M. E. & Montes-Horcasitas, M. C. Characterization of the D-xylulose 5-phosphate/D-fructose 6-phosphate phosphoketolase gene, xpkL, from Cellulomonas flavigena. J. Biotechnol. 118, S134–S134 (2005).

    Google Scholar 

  21. Liu, L. X. et al. Phosphoketolase pathway for xylose catabolism in Clostridium acetobutylicum revealed by 13C metabolic flux analysis. J. Bacteriol. 194, 5413–5422 (2012).

    Article  CAS  Google Scholar 

  22. Posthuma, C. C. et al. Expression of the xylulose 5-phosphate phosphoketolase gene, xpkA, from Lactobacillus pentosus MD363 is induced by sugars that are fermented via the phosphoketolase pathway and is repressed by glucose mediated by CcpA and the mannose phosphoenolpyruvate phosphotransferase system. Appl. Environ. Microbiol. 68, 831–837 (2002).

    Article  CAS  Google Scholar 

  23. Duan, Z. B., Shang, Y. F., Gao, Q., Zheng, P. & Wang, C. S. A phosphoketolase Mpk1 of bacterial origin is adaptively required for full virulence in the insect-pathogenic fungus Metarhizium anisopliae. Environ. Microbiol. 11, 2351–2360 (2009).

    Article  CAS  Google Scholar 

  24. Sarkar, P. & Roy, A. Molecular cloning, characterization and expression of a gene encoding phosphoketolase from Termitomyces clypeatus. Biochem. Biophys. Res. Commun. 447, 621–625 (2014).

    Article  CAS  Google Scholar 

  25. Moriyama, T., Tajima, N., Sekine, K. & Sato, N. Characterization of three putative xylulose 5-phosphate/fructose 6-phosphate phosphoketolases in the cyanobacterium Anabaena sp. PCC 7120. Biosci. Biotechnol. Biochem. 79, 767–774 (2015).

    Article  CAS  Google Scholar 

  26. Suzuki, R. et al. Crystal structures of phosphoketolase thiamine diphosphate-dependent dehydration mechanism. J. Biol. Chem. 285, 34279–34287 (2010).

    Article  CAS  Google Scholar 

  27. You, L., Berla, B., He, L., Pakrasi, B. H. & Tang, Y. J. 13C-MFA delineates the photomixotrophic metabolism of Synechocystis sp. PCC 6803 under light- and carbon-sufficient conditions. Biotechnol. J. 9, 684–692 (2014).

    Article  CAS  Google Scholar 

  28. Nakamura, Y., Kaneko, T., Hirosawa, M., Miyajima, N. & Tabata, S. CyanoBase, a WWW database containing the complete nucleotide sequence of the genome of Synechocystis sp. strain PCC6803. Nucleic Acids Res. 26, 63–67 (1998).

    Article  CAS  Google Scholar 

  29. Kucho, K. et al. Global analysis of circadian expression in the cyanobacterium Synechocystis sp strain PCC 6803. J. Bacteriol. 187, 2190–2199 (2005).

    Article  CAS  Google Scholar 

  30. Battchikova, N. et al. Dynamic changes in the proteome of Synechocystis 6803 in response to CO2 limitation revealed by quantitative proteomics. J. Proteome Res. 9, 5896–5912 (2010).

    Article  CAS  Google Scholar 

  31. Kaczmarzyk, D. & Fulda, M. Fatty acid activation in cyanobacteria mediated by acyl-acyl carrier protein synthetase enables fatty acid recycling. Plant Physiol. 152, 1598–1610 (2010).

    Article  CAS  Google Scholar 

  32. Wu, G., Bao, T., Shen, Z. & Wu, Q. Sodium acetate stimulates PHB biosynthesis in Synechocystis sp. PCC 6803. Tsinghua Sci. Technol. 7, 435–438 (2002).

    CAS  Google Scholar 

  33. Bogorad, I. W., Lin, T. S. & Liao, J. C. Synthetic non-oxidative glycolysis enables complete carbon conservation. Nature 502, 693–697 (2013).

    Article  CAS  Google Scholar 

  34. Kocharin, K., Siewers, V. & Nielsen, J. Improved polyhydroxybutyrate production by Saccharomyces cerevisiae through the use of the phosphoketolase pathway. Biotechnol. Bioeng. 110, 2216–2224 (2013).

    Article  CAS  Google Scholar 

  35. Antoniewicz, M. R., Kelleher, J. K. & Stephanopoulos, G. Elementary metabolite units (EMU): a novel framework for modeling isotopic distributions. Metab. Eng. 9, 68–86 (2007).

    Article  CAS  Google Scholar 

Download references


This work was supported by National Renewable Energy Laboratory Director's Postdoc Fellowship (to W.X.), and by the US Department of Energy (DOE), Office of Science, Basic Energy Science (to M.G., M.C., J.Y.). The latter funded in part the conception and execution of the work as well as preparation of the manuscript. It was also supported in part by the DOE Office of Energy Efficiency and Renewable Energy, Fuel Cell Technologies Office (to P.C.M.), BioEnergy Technologies Office (to E.G.), Science Undergraduate Laboratory Internship program (to S.R.), and a Dragon-Gate grant (to T.C.L.) from Ministry of Science and Technology in Taiwan. The authors acknowledge M. Seibert from NREL and A. Grossman from the Carnegie Institution for Science for helpful discussion. The software Metran was developed and kindly provided by Maciek R. Antoniewicz from the University of Delaware. The US Government retains and the publisher, by accepting the article for publication, acknowledges that the US Government retains a nonexclusive, paid up, irrevocable, worldwide license to publish or reproduce the published form of this work, or allow others to do so, for US Government purposes.

Author information

Authors and Affiliations



W.X., P.C.M., M.G. and J.Y. planned the project; W.X., T.C.L., E.G., M.C. and S.R. performed the experiments; W.X., E.G. and J.Y. analysed the data and drafted the manuscript; all authors edited the manuscript.

Corresponding author

Correspondence to Jianping Yu.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Xiong, W., Lee, TC., Rommelfanger, S. et al. Phosphoketolase pathway contributes to carbon metabolism in cyanobacteria. Nature Plants 2, 15187 (2016).

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI:

This article is cited by


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing