Systematic identification and elimination of flux bottlenecks in the aldehyde production pathway of Synechococcus elongatus PCC 7942
Open accessAbstract
Isotopically nonstationary metabolic flux analysis (INST-MFA) provides a versatile platform to quantitatively assess in vivo metabolic activities of autotrophic systems. By applying INST-MFA to recombinant aldehyde-producing cyanobacteria, we identified metabolic alterations that correlated with increased strain performance in order to guide rational metabolic engineering. We identified four reactions adjacent to the pyruvate node that varied significantly with increasing aldehyde production: pyruvate kinase (PK) and acetolactate synthase (ALS) fluxes were directly correlated with product formation, while pyruvate dehydrogenase (PDH) and phosphoenolpyruvate carboxylase (PPC) fluxes were inversely correlated. Overexpression of enzymes for PK or ALS did not result in further improvements to the previous best-performing strain, while downregulation of PDH expression (through antisense RNA expression) or PPC flux (through expression of the reverse reaction, phosphoenolpyruvate carboxykinase) provided significant improvements. These results illustrate the potential of INST-MFA to enable a systematic approach for iterative identification and removal of pathway bottlenecks in autotrophic host cells.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The streamlined genome and predictable genetic behaviour of S. elongatus PCC 7942 have facilitated the development of various synthetic biology tools, such as inducible promoters, modular genetic circuits, and genome integration systems.
“The streamlined genome and predictable genetic behaviour of S. elongatus PCC 7942 have facilitated the development of various synthetic biology tools, such as inducible promoters, modular genetic circuits, and genome integration systems.”
From Cyanobacteria as a Photosynthetic Chassis for Metabolic Pathway Engineering with Heterologous Gene Expression (2026) · cites this paper as [63]
The Results section describes a Zn²⁺-inducible expression cassette and a new genome integration site, NS4; the Methods section describes swapping different genes into that cassette. The paper does not attribute these tools to a streamlined genome or predictable genetic behaviour, and the cited passages do not describe modular genetic circuits. Page numbers are not available in our copy. (LLM, conf=0.86)
Experimental — accuracy not yet measured
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2−ΔΔCT Method
Livak, K. J., & Schmittgen, T. D. (2001) · Methods · doi:10.1006/meth.2001.1262 · Cited by 180,860 · see citing works
Mutation of the mouse klotho gene leads to a syndrome resembling ageing
Kuro-o, M., Matsumura, Y., Aizawa, H., Kawaguchi, H., Suga, T., Utsugi, T., Ohyama, Y., Kurabayashi, M., Kaname, T., Kume, E., et al. (1997) · Nature · doi:10.1038/36285 · Cited by 3,837 · see citing works
Primer3Plus, an enhanced web interface to Primer3
Untergasser, A., Nijveen, H., Rao, X., Bisseling, T., Geurts, R., & Leunissen, J. A. M. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm306 · Cited by 2,761 · see citing works
Engineering Cellular Metabolism
Nielsen, J., & Keasling, J. D. (2016) · Cell · doi:10.1016/j.cell.2016.02.004 · Cited by 1,400 · see citing works
Burgard, A. P., Pharkya, P., & Maranas, C. D. (2003) · Biotechnology and Bioengineering · doi:10.1002/bit.10803 · Cited by 1,262 · see citing works
Direct photosynthetic recycling of carbon dioxide to isobutyraldehyde
Atsumi, S., Higashide, W., & Liao, J. C. (2009) · Nature Biotechnology · doi:10.1038/nbt.1586 · Cited by 870 · see citing works
Ethanol Synthesis by Genetic Engineering in Cyanobacteria
Deng, M.-D., & Coleman, J. R. (1999) · Applied and Environmental Microbiology · doi:10.1128/aem.65.2.523-528.1999 · Cited by 457 · see citing works
Determination of confidence intervals of metabolic fluxes estimated from stable isotope measurements
Antoniewicz, M. R., Kelleher, J. K., & Stephanopoulos, G. N. (2006) · Metabolic Engineering · doi:10.1016/j.ymben.2006.01.004 · Cited by 451 · see citing works
Ranganathan, S., Suthers, P. F., & Maranas, C. D. (2010) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000744 · Cited by 420 · see citing works
INCA: a computational platform for isotopically non-stationary metabolic flux analysis
Young, J. D. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu015 · Cited by 398 · see citing works
Self-citationMapping photoautotrophic metabolism with isotopically nonstationary 13C flux analysis
Young, J. D., Shastri, A. A., Stephanopoulos, G. N., & Morgan, J. A. (2011) · Metabolic Engineering · doi:10.1016/j.ymben.2011.08.002 · Cited by 347 · see citing works
Self-citationDetailing the optimality of photosynthesis in cyanobacteria through systems biology analysis
Nogales, J., Gudmundsson, S., Knight, E. M., Palsson, B. O., & Thiele, I. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1117907109 · Cited by 301 · see citing works
Stal, L. (1997) · FEMS Microbiology Reviews · doi:10.1016/s0168-6445(97)00056-9 · Cited by 301 · see citing works
High Precision Isotope Ratio Monitoring Techniques in Mass Spectrometry
Brand, W. A. (1996) · Journal of Mass Spectrometry · doi:10.1002/(sici)1096-9888(199603)31:3 · Cited by 299 · see citing works
Metabolic engineering of cyanobacteria for the synthesis of commodity products
Angermayr, S. A., Gorchs Rovira, A., & Hellingwerf, K. J. (2015) · Trends in Biotechnology · doi:10.1016/j.tibtech.2015.03.009 · Cited by 273 · see citing works
Structure, mechanism and catalytic duality of thiamine-dependent enzymes
Frank, R., Leeper, F. J., & Luisi, B. F. (2007) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-007-6423-5 · Cited by 269 · see citing works
Accurate Assessment of Amino Acid Mass Isotopomer Distributions for Metabolic Flux Analysis
Antoniewicz, M. R., Kelleher, J. K., & Stephanopoulos, G. N. (2007) · Analytical Chemistry · doi:10.1021/ac0708893 · Cited by 257 · see citing works
An elementary metabolite unit (EMU) based method of isotopically nonstationary flux analysis
Young, J. D., Walther, J. L., Antoniewicz, M. R., Yoo, H., & Stephanopoulos, G. N. (2007) · Biotechnology and Bioengineering · doi:10.1002/bit.21632 · Cited by 257 · see citing works
Self-citationMa, F., Jazmin, L. J., Young, J. D., & Allen, D. K. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1319485111 · Cited by 230 · see citing works
Self-citationFlux Balance Analysis of Photoautotrophic Metabolism
Shastri, A. A., & Morgan, J. A. (2005) · Biotechnology Progress · doi:10.1021/bp050246d · Cited by 205 · see citing works
Physiology, Biochemistry and Genetics of Bacterial Glycogen Synthesis
Preiss, J., & Romeo, T. (1990) · Advances in microbial physiology/Advances in Microbial Physiology · doi:10.1016/s0065-2911(08)60113-7 · Cited by 189 · see citing works
Non-optimal codon usage is a mechanism to achieve circadian clock conditionality
Xu, Y. Q., Ma, P., Shah, P., Rokas, A., Liu, Y., & Johnson, C. H. (2013) · Nature · doi:10.1038/nature11942 · Cited by 174 · see citing works
Self-citationHuang, C.-H., Shen, C. R., Li, H., Sung, L.-Y., Wu, M.-Y., & Hu, Y.-C. (2016) · Microbial Cell Factories · doi:10.1186/s12934-016-0595-3 · Cited by 164 · see citing works
Egnatchik, R. A., Leamy, A. K., Noguchi, Y., Shiota, M., & Young, J. D. (2014) · Metabolism · doi:10.1016/j.metabol.2013.10.009 · Cited by 161 · see citing works
Self-citationKim, Y., Ingram, L. O., & Shanmugam, K. T. (2008) · Journal of Bacteriology · doi:10.1128/jb.00104-08 · Cited by 128 · see citing works
Circadian clock‐protein expression in cyanobacteria: rhythms and phase setting
Xu, Y., Mori, T., & Johnson, C. H. (2000) · The EMBO Journal · doi:10.1093/emboj/19.13.3349 · Cited by 128 · see citing works
Self-citationHasegawa, S., Suda, M., Uematsu, K., Natsuma, Y., Hiraga, K., Jojima, T., Inui, M., & Yukawa, H. (2012) · Applied and Environmental Microbiology · doi:10.1128/aem.02806-12 · Cited by 128 · see citing works
Plaza, M., de Palencia, P. F., Peláez, C., & Requena, T. (2004) · FEMS Microbiology Letters · doi:10.1111/j.1574-6968.2004.tb09778.x · Cited by 127 · see citing works
Broddrick, J. T., Rubin, B. E., Welkie, D. G., Du, N., Mih, N., Diamond, S., Lee, J. J., Golden, S. S., & Palsson, B. Ø. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1613446113 · Cited by 126 · see citing works
13C metabolic flux analysis: optimal design of isotopic labeling experiments
Antoniewicz, M. R. (2013) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2013.02.003 · Cited by 120 · see citing works
Buchholz, J., Schwentner, A., Brunnenkan, B., Gabris, C., Grimm, S., Gerstmeir, R., Takors, R., Eikmanns, B. J., & Blombach, B. (2013) · Applied and Environmental Microbiology · doi:10.1128/aem.01741-13 · Cited by 107 · see citing works
OpenMebius: An Open Source Software for Isotopically Nonstationary13C-Based Metabolic Flux Analysis
Kajihata, S., Furusawa, C., Matsuda, F., & Shimizu, H. (2014) · BioMed Research International · doi:10.1155/2014/627014 · Cited by 103 · see citing works
Abernathy, M. H., Yu, J., Ma, F., Liberton, M., Ungerer, J. L., Hollinshead, W. D., Gopalakrishnan, S., He, L., Maranas, C. D., Pakrasi, H. B., et al. (2017) · Biotechnology for Biofuels · doi:10.1186/s13068-017-0958-y · Cited by 102 · see citing works
Wu, C., Xiong, W., Dai, J., & Wu, Q. (2015) · Plant Physiology · doi:10.1104/pp.114.250688 · Cited by 99 · see citing works
Shastri, A. A., & Morgan, J. A. (2007) · Phytochemistry · doi:10.1016/j.phytochem.2007.03.042 · Cited by 95 · see citing works
Experimental design principles for isotopically instationary 13C labeling experiments
Nöh, K., & Wiechert, W. (2006) · Biotechnology and Bioengineering · doi:10.1002/bit.20803 · Cited by 89 · see citing works
Shabestary, K., Anfelt, J., Ljungqvist, E., Jahn, M., Yao, L., & Hudson, E. P. (2018) · ACS Synthetic Biology · doi:10.1021/acssynbio.8b00056 · Cited by 89 · see citing works
Modulation of the Major Paths of Carbon in Photorespiratory Mutants of Synechocystis
Huege, J., Goetze, J., Schwarz, D., Bauwe, H., Hagemann, M., & Kopka, J. (2011) · PLoS ONE · doi:10.1371/journal.pone.0016278 · Cited by 88 · see citing works
Metabolic responses to substrate futile cycling in Escherichia coli.
Chao, Y., & Liao, J. C. (1994) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(17)37663-9 · Cited by 84 · see citing works
van der Woude, A. D., Angermayr, S. A., Veetil, V. P., Osnato, A., & Hellingwerf, K. J. (2014) · Journal of Biotechnology · doi:10.1016/j.jbiotec.2014.04.029 · Cited by 79 · see citing works
Isotopically nonstationary 13C flux analysis of cyanobacterial isobutyraldehyde production
Jazmin, L. J., Xu, Y. Q., Cheah, Y. E., Adebiyi, A. O., Johnson, C. H., & Young, J. D. (2017) · Metabolic Engineering · doi:10.1016/j.ymben.2017.05.001 · Cited by 78 · see citing works
Self-citationRecent advances in synthetic biology of cyanobacteria
Sengupta, A., Pakrasi, H. B., & Wangikar, P. P. (2018) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-018-9046-x · Cited by 78 · see citing works
Schreiner, M. E., Fiur, D., Holátko, J., Pátek, M., & Eikmanns, B. J. (2005) · Journal of Bacteriology · doi:10.1128/jb.187.17.6005-6018.2005 · Cited by 77 · see citing works
Recent Advances in the Photoautotrophic Metabolism of Cyanobacteria: Biotechnological Implications
Veaudor, T., Blanc-Garin, V., Chenebault, C., Díaz‐Santos, E., Sassi, J., Cassier‐Chauvat, C., & Chauvat, F. (2020) · Life · doi:10.3390/life10050071 · Cited by 70 · see citing works
Isotopically nonstationary metabolic flux analysis (INST-MFA): putting theory into practice
Cheah, Y. E., & Young, J. D. (2018) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2018.02.013 · Cited by 69 · see citing works
Self-citationErbe, J. L., Taylor, K. B., & Hall, L. M. (1995) · Nucleic Acids Research · doi:10.1093/nar/23.13.2472 · Cited by 65 · see citing works
Hädicke, O., Bettenbrock, K., & Klamt, S. (2015) · Biotechnology and Bioengineering · doi:10.1002/bit.25623 · Cited by 64 · see citing works
Wang, Q., Ou, M. S., Kim, Y., et al. (2010) · Applied and Environmental Microbiology · doi:10.1128/aem.02545-09 · Cited by 62 · see citing works
Erbe, J. L., Adams, A. C., Taylor, K. B., & Hall, L. M. (1996) · Journal of Industrial Microbiology & Biotechnology · doi:10.1007/bf01570047 · Cited by 59 · see citing works
DELAPLAZA, M., FERNANDEZDEPALENCIA, P., Peláez, C., & Requena, T. (2004) · FEMS Microbiology Letters · doi:10.1016/j.femsle.2004.07.057 · Cited by 54 · see citing works
Genome Engineering of the 2,3-Butanediol Biosynthetic Pathway for Tight Regulation in Cyanobacteria
Nozzi, N. E., & Atsumi, S. (2015) · ACS Synthetic Biology · doi:10.1021/acssynbio.5b00057 · Cited by 47 · see citing works
13C flux analysis of cyanobacterial metabolism
Adebiyi, A. O., Jazmin, L. J., & Young, J. D. (2014) · Photosynthesis Research · doi:10.1007/s11120-014-0045-1 · Cited by 43 · see citing works
Self-citationA requirement for phosphoenolpyruvate carboxylase in the cyanobacterium Synechococcus PCC 7942
Luinenburg, I., & Coleman, J. R. (1990) · Archives of Microbiology · doi:10.1007/bf00245230 · Cited by 42 · see citing works
ETA: Robust software for determination of cell specific rates from extracellular time courses
Murphy, T. A., & Young, J. D. (2013) · Biotechnology and Bioengineering · doi:10.1002/bit.24836 · Cited by 41 · see citing works
Self-citationIsotopomer Measurement Techniques in Metabolic Flux Analysis II: Mass Spectrometry
Young, J. D., Allen, D. K., & Morgan, J. A. (2013) · Methods in molecular biology · doi:10.1007/978-1-62703-661-0_7 · Cited by 38 · see citing works
Self-citationPereira, A. G. M., Jazmin, L. J., & Young, J. D. (2015) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2015.08.004 · Cited by 37 · see citing works
Self-citationIsotopically Nonstationary MFA (INST-MFA) of Autotrophic Metabolism
Jazmin, L. J., O’Grady, J. P., Ma, F., et al. (2013) · Methods in molecular biology · doi:10.1007/978-1-62703-688-7_12 · Cited by 36 · see citing works
Abernathy, M. H., Czajka, J. J., Allen, D. K., Hill, N. C., Cameron, J. C., & Tang, Y. (2019) · Metabolic Engineering · doi:10.1016/j.ymben.2019.04.010 · Cited by 34 · see citing works
Jaiswal, D., Prasannan, C. B., Hendry, J. I., & Wangikar, P. P. (2018) · Analytical Chemistry · doi:10.1021/acs.analchem.7b05329 · Cited by 32 · see citing works
Wegner, A., Weindl, D., Jäger, C., Sapcariu, S. C., Dong, X., Stephanopoulos, G. N., & Hiller, K. (2014) · Analytical Chemistry · doi:10.1021/ac403879d · Cited by 30 · see citing works
Luinenburg, I., & Coleman, J. R. (1993) · PLANT PHYSIOLOGY · doi:10.1104/pp.101.1.121 · Cited by 10 · see citing works
Flagged first, then by citations
Research works printed but not linked: 1
- Cheah YE, Hasenour CM, Young JD, 2017 13C Flux Analysis in Biotechnology and Medicine Systems Biology Wiley-VCH Verlag GmbH & Co. KGaA, pp. 25– 70.
Cited by
Sorted by citations
Xie, H., Kjellström, J., & Lindblad, P. (2023) · Biotechnology for Biofuels and Bioproducts · doi:10.1186/s13068-023-02385-1 · Cited by 31 · see citing works
Application of Cyanobacteria as Chassis Cells in Synthetic Biology
Liu, X., Tang, K., & Hu, J. (2024) · Microorganisms · doi:10.3390/microorganisms12071375 · Cited by 20 · see citing works
Expressing 2-keto acid pathway enzymes significantly increases photosynthetic isobutanol production
Xie, H., & Lindblad, P. (2022) · Microbial Cell Factories · doi:10.1186/s12934-022-01738-z · Cited by 17 · see citing works
Xie, H., Bourgade, B., Stensjö, K., & Lindblad, P. (2025) · Microbial Cell Factories · doi:10.1186/s12934-025-02727-8 · Cited by 11 · see citing works
Walshe, J., & Saha, S. K. (2026) · Current Issues in Molecular Biology · doi:10.3390/cimb48060638 · Cited by 1 · see citing works
“Its combination of genetic tractability, well-characterised physiology, and relatively rapid growth rate positions S. elongatus PCC 7942 as a significant model for advancing cyanobacterial metabolic engineering strategies [63].”
- Authors
- Cheah, Y. E., Xu, Y., Sacco, S. A., Babele, P. K., Zheng, A. O., Johnson, C. H., & Young, J. D.
- Affiliations
- Vanderbilt University (US)
- Corresponding author
- Young, Jamey D.
- ORCID
- Venue
- Metabolic Engineering
- Publisher
- Elsevier BV
- Published
- 2020-07
- Volume
- 60
- Pages
- 56-65
- ISSN
- 1096-7176 (ISSN-L)
- PMC
- PMC7217728
- OpenAlex
- W3014060420
- Cited by
- 52
- References
- 61
- Citations by year
- 2026: 5 · 2025: 4 · 2024: 6 · 2023: 6 · 2022: 17 · 2021: 9 · 2020: 5
- FWCI
- 3.00
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Metabolic Engineering (acceptedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
- Funders
- National Institutes of Health (R01 GM107434, R37 GM067152)
- U.S. Department of Energy (DE-SC0019404)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial Metabolic Engineering and Bioproduction
- Physical Sciences › Energy › Renewable Energy, Sustainability and the Environment › Algal biology and biofuel production
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Plant biochemistry and biosynthesis
- Keywords
- aldehyde synthesis, Synechococcus elongatus PCC 7942, cyanobacteria, pyruvate kinase, acetolactate synthase, pyruvate dehydrogenase, phosphoenolpyruvate carboxylase, phosphoenolpyruvate carboxykinase, autotrophic production
- MeSH terms
- Acetolactate Synthase, Aldehydes, Amino Acids, Phosphoenolpyruvate Carboxylase, Pyruvate Dehydrogenase Complex, Pyruvate Kinase, Pyruvates, RNA, Bacterial, Synechococcus, Metabolic Engineering, Metabolic Flux Analysis
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
