Skip to main content
Log in

Metabolic flux analysis and metabolic engineering for polyhydroxybutyrate (PHB) production

  • REVIEW PAPER
  • Published:
Polymer Bulletin Aims and scope Submit manuscript

Abstract

Metabolic engineering provides a more sustainable alternative by using complex metabolic processes to generate valuable compounds by exploiting nature's metabolic networks. Metabolic flux analysis is frequently used in metabolic engineering to improve production yields and selectivity of compounds including biofuels, medicines, and industrial chemicals. It analyzes metabolic pathways and flux distribution to identify essential steps and targets for optimization, mainly to increase biopolymer synthesis, including polyhydroxybutyrate (PHB). PHB is a significant carbon reservoir due to its capacity to store carbon in a biodegradable polymer form in sectors such as packaging, biomedicine, and environmental remediation, making it an economically and environmentally friendly substitute to existing nonrenewable resources. Metabolic flux analysis and metabolic engineering are essential in synthesizing PHB, a biodegradable polymer with several uses. By combining these techniques, researchers can enhance efficiency, boost yields, and develop microorganisms with improved PHB synthesis capabilities. Metabolic flux analysis can identify rate-limiting steps in the PHB biosynthesis pathway and evaluate flux distribution, enabling the identification of metabolic engineering targets that may increase PHB production. Metabolic engineering may also increase the expression of PHB biosynthesis genes or add new genes to the pathway. The study analyzed here examines the significance of combining metabolic flux analysis and metabolic engineering, as well as their potential to considerably increase PHB production and improve the economic feasibility of this key biopolymer.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1

Similar content being viewed by others

References

  1. Libourel IGL, Shachar-Hill Y (2008) Metabolic flux analysis in plants: from intelligent design to rational engineering. Annu Rev Plant Biol 59:625–650. https://doi.org/10.1146/annurev.arplant.58.032806.103822

    Article  CAS  PubMed  Google Scholar 

  2. Boghigian BA, Seth G, Kiss R, Pfeifer BA (2010) Metabolic flux analysis and pharmaceutical production. Metab Eng 12:81–95. https://doi.org/10.1016/j.ymben.2009.10.004

    Article  CAS  PubMed  Google Scholar 

  3. Antoniewicz MR (2013) 13C metabolic flux analysis: Optimal design of isotopic labeling experiments. Curr Opin Biotechnol 24:1116–1121. https://doi.org/10.1016/j.copbio.2013.02.003

    Article  CAS  PubMed  Google Scholar 

  4. Schwender J, Ohlrogge J, Shachar-Hill Y (2004) Understanding flux in plant metabolic networks. Curr Opin Plant Biol 7:309–317. https://doi.org/10.1016/j.pbi.2004.03.016

    Article  CAS  PubMed  Google Scholar 

  5. Copeland WB, Bartley BA, Chandran D et al (2012) Computational tools for metabolic engineering. Metab Eng 14:270–280. https://doi.org/10.1016/j.ymben.2012.03.001

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Lee SY, Park JM, Kim TY (2011) Application of metabolic flux analysis in metabolic engineering. Methods Enzymol 498:67–93. https://doi.org/10.1016/B978-0-12-385120-8.00004-8

    Article  CAS  PubMed  Google Scholar 

  7. Antoniewicz MR (2013) Dynamic metabolic flux analysis-tools for probing transient states of metabolic networks. Curr Opin Biotechnol 24:973–978. https://doi.org/10.1016/j.copbio.2013.03.018

    Article  CAS  PubMed  Google Scholar 

  8. Kumar RR, Prasad S (2011) Metabolic engineering of bacteria. Indian J Microbiol 51:403–409. https://doi.org/10.1007/s12088-011-0172-8

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Chen X, Zhou L, Tian K et al (2013) Metabolic engineering of Escherichia coli: a sustainable industrial platform for bio-based chemical production. Biotechnol Adv 31:1200–1223. https://doi.org/10.1016/j.biotechadv.2013.02.009

    Article  CAS  PubMed  Google Scholar 

  10. Gao J, Du M, Zhao J et al (2022) Design of a genetically encoded biosensor to establish a high-throughput screening platform for L-cysteine overproduction. Metab Eng 73:144–157. https://doi.org/10.1016/j.ymben.2022.07.007

    Article  CAS  PubMed  Google Scholar 

  11. Liu R, Bassalo MC, Zeitoun RI, Gill RT (2015) Genome scale engineering techniques for metabolic engineering. Metab Eng 32:143–154. https://doi.org/10.1016/j.ymben.2015.09.013

    Article  CAS  PubMed  Google Scholar 

  12. Wang Y, Wondisford FE, Song C et al (2020) Metabolic flux analysis—linking isotope labeling and metabolic fluxes. Metabolites 10:1–21. https://doi.org/10.3390/metabo10110447

    Article  CAS  Google Scholar 

  13. Metallo CM, Walther JL, Stephanopoulos G (2009) Evaluation of 13C isotopic tracers for metabolic flux analysis in mammalian cells. J Biotechnol 144:167–174. https://doi.org/10.1016/j.jbiotec.2009.07.010

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Orman MA, Berthiaume F, Androulakis IP, Ierapetritou MG (2011) Advanced stoichiometric analysis of metabolic networks of mammalian systems. Crit Rev Biomed Eng 39:511–534. https://doi.org/10.1615/CritRevBiomedEng.v39.i6.30

    Article  PubMed  PubMed Central  Google Scholar 

  15. Orth JD, Thiele I, Palsson BO (2010) What is flux balance analysis? Nat Biotechnol 28:245–248. https://doi.org/10.1038/nbt.1614

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Sun S, Ding Y, Liu M et al (2020) Comparison of glucose, acetate and ethanol as carbon resource for production of poly(3-Hydroxybutyrate) and other Acetyl-CoA derivatives. Front Bioeng Biotechnol. https://doi.org/10.3389/fbioe.2020.00833

    Article  PubMed  PubMed Central  Google Scholar 

  17. Wang Q, Liu C, Xian M et al (2012) Biosynthetic pathway for poly(3-Hydroxypropionate) in recombinant Escherichia coli. J Microbiol 50:693–697. https://doi.org/10.1007/s12275-012-2234-y

    Article  CAS  PubMed  Google Scholar 

  18. Liu XW, Wang HH, Chen JY et al (2009) Biosynthesis of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) by recombinant Escherichia coli harboring propionyl-CoA synthase gene (prpE) or propionate permease gene (prpP). Biochem Eng J 43:72–77. https://doi.org/10.1016/j.bej.2008.09.001

    Article  CAS  Google Scholar 

  19. Taguchi K, Aoyagi Y, Matsusaki H et al (1999) Over-expression of 3-ketoacyl-ACP synthase III or malonyl-CoA-ACP transacylase gene induces monomer supply for polyhydroxybutyrate production in Escherichia coli HB101. Biotechnol Lett 21:579–584. https://doi.org/10.1023/A:1005572526080

    Article  CAS  Google Scholar 

  20. Kim M, Baek J, Lee J (2006) Comparison of H2H2 accumulation by Rhodobacter sphaeroides KD131 and its uptake hydrogenase and PHB synthase deficient mutant. Int J Hydrog Energy 31:121–127. https://doi.org/10.1016/j.ijhydene.2004.10.023

    Article  CAS  Google Scholar 

  21. Wang Z, Qin W, Bao S et al (2013) The influences of aerobic and anaerobic conditions on PHB and glycerin yields in the process of lignin degradation by Pseudomonas stutzeri P156. Adv Mater Res 634–638:1170–1174. https://doi.org/10.4028/www.scientific.net/AMR.634-638.1170

    Article  CAS  Google Scholar 

  22. Towijit U, Songruk N, Lindblad P et al (2018) Co-overexpression of native phospholipid-biosynthetic genes plsX and plsC enhances lipid production in Synechocystis sp. PCC 6803. Sci Rep. https://doi.org/10.1038/s41598-018-31789-5

    Article  PubMed  PubMed Central  Google Scholar 

  23. Muller EEL, Sheik AR, Wilmes P (2014) Lipid-based biofuel production from wastewater. Curr Opin Biotechnol 30:9–16. https://doi.org/10.1016/j.copbio.2014.03.007

    Article  CAS  PubMed  Google Scholar 

  24. Haywood GW, Anderson AJ, Chu L, Dawes EA (1988) The role of NADH- and NADPH-linked acetoacetyl-CoA reductases in the poly-3-hydroxybutyrate synthesizing organism Alcaligenes eutrophus. FEMS Microbiol Lett 52:259–264. https://doi.org/10.1111/j.1574-6968.1988.tb02607.x

    Article  CAS  Google Scholar 

  25. Gradinaru VR (2005) Acyl-CoA dehydrogenases: mechanistic studies on medium chain Acyl-CoA dehydrogenase dissertation. Bach

  26. Tan HT, Chek MF, Miyahara Y et al (2022) Characterization of an (R)-specific enoyl-CoA hydratase from streptomyces sp. strain CFMR 7: A metabolic tool for enhancing the production of poly(3-hydroxybutyrate-co-3-hydroxyhexanoate). J Biosci Bioeng 134:288–294. https://doi.org/10.1016/j.jbiosc.2022.07.005

    Article  CAS  PubMed  Google Scholar 

  27. Volodina E, Steinbüchel A (2014) (S)-3-hydroxyacyl-CoA dehydrogenase/enoyl-CoA hydratase (FadB’) from fatty acid degradation operon of Ralstonia eutropha H16. AMB Express 4:1–9. https://doi.org/10.1186/s13568-014-0069-0

    Article  CAS  Google Scholar 

  28. Segura D, Vargas E, Espín G (2000) β-Ketothiolase genes in Azotobacter vinelandii. Gene 260:113–120. https://doi.org/10.1016/S0378-1119(00)00462-5

    Article  CAS  PubMed  Google Scholar 

  29. Tang R, Peng X, Weng C, Han Y (2022) The overexpression of phasin and regulator genes promoting the synthesis of polyhydroxybutyrate in cupriavidus necator H16 under nonstress conditions. Appl Environ Microbiol. https://doi.org/10.1128/AEM.01458-21

    Article  PubMed  PubMed Central  Google Scholar 

  30. Tang R, Weng C, Peng X, Han Y (2020) Metabolic engineering of Cupriavidus necator H16 for improved chemoautotrophic growth and PHB production under oxygen-limiting conditions. Metab Eng 61:11–23. https://doi.org/10.1016/j.ymben.2020.04.009

    Article  CAS  PubMed  Google Scholar 

  31. Aristya GR, Lin YJ, Chang JS et al (2022) Polyhydroxybutyrate (PHB) production from crude glycerol by genetic engineering of Rhodotorula glutinis. Bioresour Technol Rep. https://doi.org/10.1016/j.biteb.2022.101048

    Article  Google Scholar 

  32. John ME, Keller G (1996) Metabolic pathway engineering in cotton: Biosynthesis of polyhydroxybutyrate in fiber cells. Proc Natl Acad Sci U S A 93:12768–12773. https://doi.org/10.1073/pnas.93.23.12768

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Koch M, Bruckmoser J, Scholl J et al (2020) Maximizing PHB content in Synechocystis sp. PCC 6803: a new metabolic engineering strategy based on the regulator PirC. Microb Cell Fact. https://doi.org/10.1186/s12934-020-01491-1

    Article  PubMed  PubMed Central  Google Scholar 

  34. Matsumoto K, Morimoto K, Gohda A et al (2011) Improved polyhydroxybutyrate (PHB) production in transgenic tobacco by enhancing translation efficiency of bacterial PHB biosynthetic genes. J Biosci Bioeng 111:485–488. https://doi.org/10.1016/j.jbiosc.2010.11.020

    Article  CAS  PubMed  Google Scholar 

  35. Müller-Santos M, Koskimäki JJ, Alves LPS et al (2021) The protective role of PHB and its degradation products against stress situations in bacteria. FEMS Microbiol Rev. https://doi.org/10.1093/femsre/fuaa058

    Article  PubMed  Google Scholar 

  36. Nishihata S, Kondo T, Tanaka K et al (2018) Bradyrhizobium diazoefficiens USDA110 PhaR functions for pleiotropic regulation of cellular processes besides PHB accumulation. BMC Microbiol. https://doi.org/10.1186/s12866-018-1317-2

    Article  PubMed  PubMed Central  Google Scholar 

  37. Lee TR, Lin JS, Wang SS, Shaw GC (2004) PhaQ, a new class of poly-β-hydroxybutyrate (PHB)-responsive repressor, regulates phaQ and phaP (Phasin) expression in Bacillus megaterium through Interaction with PHB. J Bacteriol 186:3015–3021. https://doi.org/10.1128/JB.186.10.3015-3021.2004

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Pfeiffer D, Jendrossek D (2014) PhaM Is the Physiological Activator of Poly(3-Hydroxybutyrate) (PHB) Synthase (PhaC1) in Ralstonia eutropha. Appl Environ Microbiol 80:555–563. https://doi.org/10.1128/AEM.02935-13

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Lee YR, Nur Fitriana H, Lee SY et al (2020) Molecular profiling and optimization studies for growth and phb production conditions in Rhodobacter sphaeroides. Energies. https://doi.org/10.3390/en13236471

    Article  PubMed  PubMed Central  Google Scholar 

  40. Xie J, Zhou J, Zhang H, Li Y (2011) Increasing reductant NADPH content via metabolic engineering of PHB synthesis pathway in Synechocystis sp. PCC 6803. Shengwu Gongcheng Xuebao/Chin J Biotechnol 27:998–1004

    CAS  Google Scholar 

  41. Park YL, Song HS, Choi TR et al (2021) Revealing of sugar utilization systems in Halomonas sp. YLGW01 and application for poly(3-hydroxybutyrate) production with low-cost medium and easy recovery. Int J Biol Macromol 167:151–159. https://doi.org/10.1016/j.ijbiomac.2020.11.163

    Article  CAS  PubMed  Google Scholar 

  42. Tumlirsch T, Sznajder A, Jendrossek D (2015) Formation of polyphosphate by polyphosphate kinases and its relationship to poly(3-hydroxybutyrate) accumulation in Ralstonia eutropha strain H16. Appl Environ Microbiol 81:8277–8293. https://doi.org/10.1128/AEM.02279-15

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Handrick R, Reinhardt S, Kimmig P, Jendrossek D (2004) The “intracellular” poly(3-hydroxybutyrate) (PHB) depolymerase of Rhodospirillum rubrum is a periplasm-located protein with specificity for native PHB and with structural similarity to extracellular PHB depolymerases. J Bacteriol 186:7243–7253. https://doi.org/10.1128/JB.186.21.7243-7253.2004

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Kobayashi T, Shiraki M, Abe T et al (2003) Purification and properties of an intracellular 3-hydroxybutyrate-oligomer hydrolase (PhaZ2) in Ralstonia eutropha H16 and its identification as a novel intracellular poly(3-hydroxybutyrate) depolymerase. J Bacteriol 185:3485–3490. https://doi.org/10.1128/JB.185.12.3485-3490.2003

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. de las Heras AM, Portugal-Nunes DJ, Rizza N et al (2016) Anaerobic poly-3-d-hydroxybutyrate production from xylose in recombinant Saccharomyces cerevisiae using a NADH-dependent acetoacetyl-CoA reductase. Microb Cell Fact. https://doi.org/10.1186/s12934-016-0598-0

    Article  PubMed  PubMed Central  Google Scholar 

  46. Shi LL, Da YY, Zheng WT et al (2020) Production of polyhydroxyalkanoate from acetate by metabolically engineered Aeromonas hydrophilia. J Biosci Bioeng 130:290–294. https://doi.org/10.1016/j.jbiosc.2020.05.003

    Article  CAS  PubMed  Google Scholar 

  47. Poole P, Allaway D (2000) Carbon and nitrogen metabolism in Rhizobium. In: Advances in microbial physiology. pp 117–163

  48. Lin Z, Zhang Y, Yuan Q et al (2015) Metabolic engineering of Escherichia coli for poly(3-hydroxybutyrate) production via threonine bypass. Microb Cell Fact 14:185. https://doi.org/10.1186/s12934-015-0369-3

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Park S, Kim GB, Kim HU et al (2019) Enhanced production of poly-3-hydroxybutyrate (PHB) by expression of response regulator DR1558 in recombinant Escherichia coli. Int J Biol Macromol 131:29–35. https://doi.org/10.1016/j.ijbiomac.2019.03.044

    Article  CAS  PubMed  Google Scholar 

  50. Ku JT, Chen AY, Lan EI (2020) Metabolic engineering design strategies for increasing acetyl-coa flux. Metabolites. https://doi.org/10.3390/metabo10040166

    Article  PubMed  PubMed Central  Google Scholar 

  51. Yishai O, Goldbach L, Tenenboim H et al (2017) Engineered assimilation of exogenous and endogenous formate in Escherichia coli. ACS Synth Biol 6:1722–1731. https://doi.org/10.1021/acssynbio.7b00086

    Article  CAS  PubMed  Google Scholar 

  52. Zhao Y, Jian X, Wu J et al (2019) Elucidation of the biosynthesis pathway and heterologous construction of a sustainable route for producing umbelliferone. J Biol Eng. https://doi.org/10.1186/s13036-019-0174-3

    Article  PubMed  PubMed Central  Google Scholar 

  53. Kocharin K, Chen Y, Siewers V, Nielsen J (2012) Engineering of acetyl-CoA metabolism for the improved production of polyhydroxybutyrate in Saccharomyces cerevisiae. AMB Express. https://doi.org/10.1186/2191-0855-2-52

    Article  PubMed  PubMed Central  Google Scholar 

  54. Edwards CB, Copes N, Brito AG et al (2013) Malate and Fumarate Extend Lifespan in Caenorhabditis elegans. PLoS ONE. https://doi.org/10.1371/journal.pone.0058345

    Article  PubMed  PubMed Central  Google Scholar 

  55. Kabir MM, Shimizu K (2003) Gene expression patterns for metabolic pathway in pgi knockout Escherichia coli with and without phb genes based on RT-PCR. J Biotechnol 105:11–31. https://doi.org/10.1016/S0168-1656(03)00170-6

    Article  CAS  PubMed  Google Scholar 

  56. Naranjo JM, Posada JA, Higuita JC, Cardona CA (2013) Valorization of glycerol through the production of biopolymers: The PHB case using Bacillus megaterium. Bioresour Technol 133:38–44. https://doi.org/10.1016/j.biortech.2013.01.129

    Article  CAS  PubMed  Google Scholar 

  57. de Souza L, Manasa Y, Shivakumar S (2020) Bioconversion of lignocellulosic substrates for the production of polyhydroxyalkanoates. Biocatal Agric Biotechnol. https://doi.org/10.1016/j.bcab.2020.101754

    Article  Google Scholar 

  58. Johnson K, Kleerebezem R, van Loosdrecht MCM (2010) Influence of the C/N ratio on the performance of polyhydroxybutyrate (PHB) producing sequencing batch reactors at short SRTs. Water Res 44:2141–2152. https://doi.org/10.1016/j.watres.2009.12.031

    Article  CAS  PubMed  Google Scholar 

  59. Yim SS, Choi JW, Lee YJ, Jeong KJ (2023) Rapid combinatorial rewiring of metabolic networks for enhanced poly(3-hydroxybutyrate) production in Corynebacterium glutamicum. Microb Cell Fact. https://doi.org/10.1186/s12934-023-02037-x

    Article  PubMed  PubMed Central  Google Scholar 

  60. Wang J, Chen Z, Deng X et al (2023) Engineering Escherichia coli for Poly-β-hydroxybutyrate production from methanol. Bioengineering. https://doi.org/10.3390/bioengineering10040415

    Article  PubMed  PubMed Central  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Contributions

BS involved in sourcing data and writing of manuscript. SB involved in sourcing data and writing of manuscript. RT involved in writing of manuscript. LMS involved in designing the manuscript, reviewing the manuscript, and sourcing of data.

Corresponding author

Correspondence to Lilly M. Saleena.

Ethics declarations

Conflict of interest

The authors of this manuscript have no affiliations or involvement in any entity or organization with any financial or non-financial interest in the subject discussed in this manuscript.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Subramanian, B., Basak, S., Thirumurugan, R. et al. Metabolic flux analysis and metabolic engineering for polyhydroxybutyrate (PHB) production. Polym. Bull. (2024). https://doi.org/10.1007/s00289-024-05215-y

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s00289-024-05215-y

Keywords

Navigation