Isotopically nonstationary 13C flux analysis of cyanobacterial isobutyraldehyde production

Jazmin, Lara J.; Xu, Yao; Cheah, Yi Ern; Adebiyi, Adeola O.; Johnson, Carl Hirschie; Young, Jamey D.

doi:10.1016/j.ymben.2017.05.001

Title: Isotopically nonstationary ¹³C flux analysis of cyanobacterial isobutyraldehyde production

Journal Article · Thu May 04 00:00:00 EDT 2017 · Metabolic Engineering

DOI:https://doi.org/10.1016/j.ymben.2017.05.001· OSTI ID:1462034

Jazmin, Lara J. ^[1]; Xu, Yao ^[1]; Cheah, Yi Ern ^[1]; Adebiyi, Adeola O. ^[1]; Johnson, Carl Hirschie ^[1]; Young, Jamey D. ^[1]

Vanderbilt Univ., Nashville, TN (United States)

Here, we applied isotopically nonstationary ¹³C metabolic flux analysis (INST-MFA) to compare the pathway fluxes of wild-type (WT) Synechococcus elongatus PCC 7942 to an engineered strain (SA590) that produces isobutyraldehyde (IBA). The flux maps revealed a potential bottleneck at the pyruvate kinase (PK) reaction step that was associated with diversion of flux into a three-step PK bypass pathway involving the enzymes PEP carboxylase (PEPC), malate dehydrogenase (MDH), and malic enzyme (ME). Overexpression of pk in SA590 led to a significant improvement in IBA specific productivity. Single-gene overexpression of the three enzymes in the proposed PK bypass pathway also led to improvements in IBA production, although to a lesser extent than pk overexpression. Combinatorial overexpression of two of the three genes in the proposed PK bypass pathway (mdh and me) led to improvements in specific productivity that were similar to those achieved by single-gene pk overexpression. Our work demonstrates how ¹³C flux analysis can be used to identify potential metabolic bottlenecks and novel metabolic routes, and how these findings can guide rational metabolic engineering of cyanobacteria for increased production of desired molecules.

View Accepted Manuscript (DOE)

View Accepted Manuscript (Publisher)

Cite

Export

Save

Research Organization:: Vanderbilt Univ., Nashville, TN (United States)

Sponsoring Organization:: USDOE

Grant/Contract Number:: SC0008118; AC05-06OR23100; P200A090323

OSTI ID:: 1462034

Alternate ID(s):: OSTI ID: 1397026

Journal Information:: Metabolic Engineering, Vol. 42, Issue C; ISSN 1096-7176

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

Citation Metrics:

Cited by: 50 works

Citation information provided by
Web of Science

References (45)

Exploring metabolic engineering design principles for the photosynthetic production of lactic acid by Synechocystis sp. PCC6803 Angermayr, S.; van der Woude, Aniek D.; Correddu, Danilo Biotechnology for Biofuels, Vol. 7, Issue 1 https://doi.org/10.1186/1754-6834-7-99	journal	January 2014
Metabolic engineering of cyanobacteria for the synthesis of commodity products Angermayr, S. Andreas; Gorchs Rovira, Aleix; Hellingwerf, Klaas J. Trends in Biotechnology, Vol. 33, Issue 6 https://doi.org/10.1016/j.tibtech.2015.03.009	journal	June 2015
Determination of confidence intervals of metabolic fluxes estimated from stable isotope measurements Antoniewicz, Maciek R.; Kelleher, Joanne K.; Stephanopoulos, Gregory Metabolic Engineering, Vol. 8, Issue 4 https://doi.org/10.1016/j.ymben.2006.01.004	journal	July 2006
Accurate Assessment of Amino Acid Mass Isotopomer Distributions for Metabolic Flux Analysis Antoniewicz, Maciek R.; Kelleher, Joanne K.; Stephanopoulos, Gregory Analytical Chemistry, Vol. 79, Issue 19 https://doi.org/10.1021/ac0708893	journal	October 2007
Direct photosynthetic recycling of carbon dioxide to isobutyraldehyde Atsumi, Shota; Higashide, Wendy; Liao, James C. Nature Biotechnology, Vol. 27, Issue 12, p. 1177-1180 https://doi.org/10.1038/nbt.1586	journal	November 2009
Bio-based production of chemicals, materials and fuels – Corynebacterium glutamicum as versatile cell factory Becker, Judith; Wittmann, Christoph Current Opinion in Biotechnology, Vol. 23, Issue 4 https://doi.org/10.1016/j.copbio.2011.11.012	journal	August 2012
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 Bricker, T. M.; Zhang, S.; Laborde, S. M. Journal of Bacteriology, Vol. 186, Issue 23 https://doi.org/10.1128/JB.186.23.8144-8148.2004	journal	November 2004
Unique attributes of cyanobacterial metabolism revealed by improved genome-scale metabolic modeling and essential gene analysis Broddrick, Jared T.; Rubin, Benjamin E.; Welkie, David G. Proceedings of the National Academy of Sciences, Vol. 113, Issue 51 https://doi.org/10.1073/pnas.1613446113	journal	December 2016
Engineered Transcriptional Systems for Cyanobacterial Biotechnology Camsund, Daniel; Lindblad, Peter Frontiers in Bioengineering and Biotechnology, Vol. 2 https://doi.org/10.3389/fbioe.2014.00040	journal	October 2014
A Simple Method for the Isolation and Purification of Total Lipides from Animal Tissues Folch, Jordi; Lees, M.; Stanley, G. H. Sloane Journal of Biological Chemistry, Vol. 226, Issue 1 https://doi.org/10.1016/S0021-9258(18)64849-5	journal	May 1957
A comparative study of the NADP-malic enzymes from Drosophila and chick liver Geer, B. W.; Krochko, D.; Oliver, M. J. Comparative Biochemistry and Physiology Part B: Comparative Biochemistry, Vol. 65, Issue 1 https://doi.org/10.1016/0305-0491(80)90109-1	journal	January 1980
Engineering cyanobacteria as photosynthetic feedstock factories Hays, Stephanie G.; Ducat, Daniel C. Photosynthesis Research, Vol. 123, Issue 3 https://doi.org/10.1007/s11120-014-9980-0	journal	February 2014
Isotopically Nonstationary MFA (INST-MFA) of Autotrophic Metabolism Jazmin, Lara J.; O’Grady, John P.; Ma, Fangfang Plant Metabolic Flux Analysis https://doi.org/10.1007/978-1-62703-688-7_12	book	October 2013
CO ₂ CONCENTRATING MECHANISMS IN PHOTOSYNTHETIC MICROORGANISMS Kaplan, Aaron; Reinhold, Leonora Annual Review of Plant Physiology and Plant Molecular Biology, Vol. 50, Issue 1 https://doi.org/10.1146/annurev.arplant.50.1.539	journal	June 1999
Structural and Regulatory Properties of Pyruvate Kinase from the Cyanobacterium Synechococcus PCC 6301 Knowles, Vicki L.; Smith, Catherine S.; Smith, Christopher R. Journal of Biological Chemistry, Vol. 276, Issue 24 https://doi.org/10.1074/jbc.M008878200	journal	April 2001
Strain improvement by metabolic engineering: lysine production as a case study for systems biology Koffas, Mattheos; Stephanopoulos, Gregory Current Opinion in Biotechnology, Vol. 16, Issue 3 https://doi.org/10.1016/j.copbio.2005.04.010	journal	June 2005
Quantifying Biomass Composition by Gas Chromatography/Mass Spectrometry Long, Christopher P.; Antoniewicz, Maciek R. Analytical Chemistry, Vol. 86, Issue 19 https://doi.org/10.1021/ac502734e	journal	September 2014
Cyanobacterial biofuel production Machado, Iara M. P.; Atsumi, Shota Journal of Biotechnology, Vol. 162, Issue 1 https://doi.org/10.1016/j.jbiotec.2012.03.005	journal	November 2012
Synthetic Biology Toolbox for Controlling Gene Expression in the Cyanobacterium Synechococcus sp. strain PCC 7002 Markley, Andrew L.; Begemann, Matthew B.; Clarke, Ryan E. ACS Synthetic Biology, Vol. 4, Issue 5 https://doi.org/10.1021/sb500260k	journal	September 2014
Engineering Synechococcus elongatus PCC 7942 for Continuous Growth under Diurnal Conditions McEwen, Jordan T.; Machado, Iara M. P.; Connor, Michael R. Applied and Environmental Microbiology, Vol. 79, Issue 5 https://doi.org/10.1128/AEM.03326-12	journal	December 2012
Solar energy conversion efficiencies in photosynthesis: Minimizing the chlorophyll antennae to maximize efficiency Melis, Anastasios Plant Science, Vol. 177, Issue 4 https://doi.org/10.1016/j.plantsci.2009.06.005	journal	October 2009
ETA: Robust software for determination of cell specific rates from extracellular time courses Murphy, Taylor A.; Young, Jamey D. Biotechnology and Bioengineering, Vol. 110, Issue 6 https://doi.org/10.1002/bit.24836	journal	January 2013
Engineering Cyanobacteria To Synthesize and Export Hydrophilic Products Niederholtmeyer, H.; Wolfstadter, B. T.; Savage, D. F. Applied and Environmental Microbiology, Vol. 76, Issue 11 https://doi.org/10.1128/AEM.00202-10	journal	April 2010
Genome Engineering of the 2,3-Butanediol Biosynthetic Pathway for Tight Regulation in Cyanobacteria Nozzi, Nicole E.; Atsumi, Shota ACS Synthetic Biology, Vol. 4, Issue 11 https://doi.org/10.1021/acssynbio.5b00057	journal	May 2015
Cyanobacteria as a Platform for Biofuel Production Nozzi, Nicole E.; Oliver, John W. K.; Atsumi, Shota Frontiers in Bioengineering and Biotechnology, Vol. 1 https://doi.org/10.3389/fbioe.2013.00007	journal	January 2013
Metabolic design for cyanobacterial chemical synthesis Oliver, John W. K.; Atsumi, Shota Photosynthesis Research, Vol. 120, Issue 3 https://doi.org/10.1007/s11120-014-9997-4	journal	April 2014
A carbon sink pathway increases carbon productivity in cyanobacteria Oliver, John W. K.; Atsumi, Shota Metabolic Engineering, Vol. 29 https://doi.org/10.1016/j.ymben.2015.03.006	journal	May 2015
Metabolic and Transcriptomic Phenotyping of Inorganic Carbon Acclimation in the Cyanobacterium Synechococcus elongatus PCC 7942 Schwarz, Doreen; Nodop, Anke; Hüge, Jan Plant Physiology, Vol. 155, Issue 4 https://doi.org/10.1104/pp.110.170225	journal	January 2011
Recent Applications of Metabolomics Toward Cyanobacteria Schwarz, Doreen; Orf, Isabel; Kopka, Joachim Metabolites, Vol. 3, Issue 1 https://doi.org/10.3390/metabo3010072	journal	February 2013
Flux Balance Analysis of Photoautotrophic Metabolism Shastri, A. A.; Morgan, J. A. Biotechnology Progress, Vol. 21, Issue 6 https://doi.org/10.1021/bp050246d	journal	December 2005
Engineering direct conversion of CO2 to biofuel Sheehan, John Nature Biotechnology, Vol. 27, Issue 12 https://doi.org/10.1038/nbt1209-1128	journal	December 2009
Picosecond spectroscopy of the charge separation in reaction centers of Chloroflexus aurantiacus with selective excitation of the primary electron donor Shuvalov, V. A.; Vasmel, H.; Amesz, J. Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 851, Issue 3 https://doi.org/10.1016/0005-2728(86)90072-1	journal	October 1986
Isolation, characterization, and physiological role of the pyruvate dehydrogenase complex and alpha-acetolactate synthase of Lactococcus lactis subsp. lactis bv. diacetylactis Snoep, J. L.; Teixeira de Mattos, M. J.; Starrenburg, M. J. Journal of Bacteriology, Vol. 174, Issue 14 https://doi.org/10.1128/JB.174.14.4838-4841.1992	journal	July 1992
Metabolic Engineering of Synechocystis sp. Strain PCC 6803 for Isobutanol Production Varman, Arul M.; Xiao, Yi; Pakrasi, Himadri B. Applied and Environmental Microbiology, Vol. 79, Issue 3 https://doi.org/10.1128/AEM.02827-12	journal	November 2012
Engineering cyanobacteria for photosynthetic production of 3-hydroxybutyrate directly from CO2 Wang, Bo; Pugh, Shawn; Nielsen, David R. Metabolic Engineering, Vol. 16 https://doi.org/10.1016/j.ymben.2013.01.001	journal	March 2013
Engineering cyanobacteria to improve photosynthetic production of alka(e)nes Wang, Weihua; Liu, Xufeng; Lu, Xuefeng Biotechnology for Biofuels, Vol. 6, Issue 1 https://doi.org/10.1186/1754-6834-6-69	journal	January 2013
Non-optimal codon usage is a mechanism to achieve circadian clock conditionality Xu, Yao; Ma, Peijun; Shah, Premal Nature, Vol. 495, Issue 7439 https://doi.org/10.1038/nature11942	journal	February 2013
Integration of the information from gene expression and metabolic fluxes for the analysis of the regulatory mechanisms in Synechocystis C., Yang; Q., Hua; K., Shimizu Applied Microbiology and Biotechnology, Vol. 58, Issue 6 https://doi.org/10.1007/s00253-002-0949-0	journal	May 2002
Metabolic Flux Analysis in Synechocystis Using Isotope Distribution from 13C-Labeled Glucose Yang, C. Metabolic Engineering, Vol. 4, Issue 3 https://doi.org/10.1006/mben.2002.0226	journal	July 2002
Quantitative analysis of intracellular metabolic fluxes using GC-MS and two-dimensional NMR spectroscopy Yang, Chen; Hua, Qiang; Shimizu, Kazuyuki Journal of Bioscience and Bioengineering, Vol. 93, Issue 1 https://doi.org/10.1016/S1389-1723(02)80058-5	journal	January 2002
¹³ C-MFA delineates the photomixotrophic metabolism of Synechocystis sp. PCC 6803 under light- and carbon-sufficient conditions You, Le; Berla, Bert; He, Lian Biotechnology Journal, Vol. 9, Issue 5 https://doi.org/10.1002/biot.201300477	journal	April 2014
INCA: a computational platform for isotopically non-stationary metabolic flux analysis Young, J. D. Bioinformatics, Vol. 30, Issue 9 https://doi.org/10.1093/bioinformatics/btu015	journal	January 2014
An elementary metabolite unit (EMU) based method of isotopically nonstationary flux analysis Young, Jamey D.; Walther, Jason L.; Antoniewicz, Maciek R. Biotechnology and Bioengineering, Vol. 99, Issue 3 https://doi.org/10.1002/bit.21632	journal	February 2008
Mapping photoautotrophic metabolism with isotopically nonstationary 13C flux analysis Young, Jamey D.; Shastri, Avantika A.; Stephanopoulos, Gregory Metabolic Engineering, Vol. 13, Issue 6 https://doi.org/10.1016/j.ymben.2011.08.002	journal	November 2011
Improving Photosynthetic Efficiency for Greater Yield Zhu, Xin-Guang; Long, Stephen P.; Ort, Donald R. Annual Review of Plant Biology, Vol. 61, Issue 1 https://doi.org/10.1146/annurev-arplant-042809-112206	journal	June 2010

Cited By (11)

A method to compute instantaneous oxygen evolution rates in cyanobacterial cultures grown in shake flasks Sengupta, Annesha; Wangikar, Pramod P. Engineering Reports, Vol. 2, Issue 1 https://doi.org/10.1002/eng2.12094	journal	January 2020
An improved method for extraction of polar and charged metabolites from cyanobacteria Prasannan, Charulata B.; Jaiswal, Damini; Davis, Rose PLOS ONE, Vol. 13, Issue 10 https://doi.org/10.1371/journal.pone.0204273	journal	October 2018
Deciphering cyanobacterial phenotypes for fast photoautotrophic growth via isotopically nonstationary metabolic flux analysis Abernathy, Mary H.; Yu, Jingjie; Ma, Fangfang Biotechnology for Biofuels, Vol. 10, Issue 1 https://doi.org/10.1186/s13068-017-0958-y	journal	November 2017
Engineering and systems-level analysis of Pseudomonas chlororaphis for production of phenazine-1-carboxamide using glycerol as the cost-effective carbon source Yao, Ruilian; Pan, Keli; Peng, Huasong Biotechnology for Biofuels, Vol. 11, Issue 1 https://doi.org/10.1186/s13068-018-1123-y	journal	May 2018
The challenge and potential of photosynthesis: unique considerations for metabolic flux measurements in photosynthetic microorganisms Sake, Cara L.; Metcalf, Alexander J.; Boyle, Nanette R. Biotechnology Letters, Vol. 41, Issue 1 https://doi.org/10.1007/s10529-018-2622-4	journal	November 2018
Model metabolic strategy for heterotrophic bacteria in the cold ocean based on Colwellia psychrerythraea 34H Czajka, Jeffrey J.; Abernathy, Mary H.; Benites, Veronica T. Proceedings of the National Academy of Sciences, Vol. 115, Issue 49 https://doi.org/10.1073/pnas.1807804115	journal	November 2018
Elevated carbon dioxide levels lead to proteome-wide alterations for optimal growth of a fast-growing cyanobacterium, Synechococcus elongatus PCC 11801 Mehta, Kanika; Jaiswal, Damini; Nayak, Monalisha Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-019-42576-1	journal	April 2019
13C metabolic flux analysis-guided metabolic engineering of Escherichia coli for improved acetol production from glycerol Yao, Ruilian; Li, Jiawei; Feng, Lei Biotechnology for Biofuels, Vol. 12, Issue 1 https://doi.org/10.1186/s13068-019-1372-4	journal	February 2019
Applications of stable isotope-based metabolomics and fluxomics toward synthetic biology of cyanobacteria Babele, Piyoosh Kumar; Young, Jamey D. Wiley Interdisciplinary Reviews: Systems Biology and Medicine, Vol. 12, Issue 3 https://doi.org/10.1002/wsbm.1472	journal	December 2019
A Novel Cyanobacterium Synechococcus elongatus PCC 11802 has Distinct Genomic and Metabolomic Characteristics Compared to its Neighbor PCC 11801 Jaiswal, Damini; Sengupta, Annesha; Sengupta, Shinjinee Scientific Reports, Vol. 10, Issue 1 https://doi.org/10.1038/s41598-019-57051-0	journal	January 2020
Metabolic engineering strategies for enhanced shikimate biosynthesis: current scenario and future developments Bilal, Muhammad; Wang, Songwei; Iqbal, Hafiz M. N. Applied Microbiology and Biotechnology, Vol. 102, Issue 18 https://doi.org/10.1007/s00253-018-9222-z	journal	July 2018

Similar Records

Metabolic engineering of Synechococcus elongatus 7942 for enhanced sucrose biosynthesis

Journal Article · Sat Sep 09 00:00:00 EDT 2023 · Metabolic Engineering · OSTI ID:1462034

Wang, Bo; Zuniga, Cristal; Guarnieri, Michael T.; +3 more

Enhancing metabolic flux to photosynthetic biofuels

Technical Report · Sat Sep 08 00:00:00 EDT 2018 · OSTI ID:1462034

Young, Jamey D.; Cheah, Yi Ern

OptSSeq explores enzyme expression and function landscapes to maximize isobutanol production rate

Journal Article · Fri Mar 01 00:00:00 EST 2019 · Metabolic Engineering · OSTI ID:1462034

Ghosh, Indro N.; Martien, Julia; Hebert, Alexander S.; +4 more

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
Synechococcus elongatus PCC7942
Isobutyraldehyde
Photoautotrophic metabolism
Nonstationary 13C metabolic flux analysis
13C INST-MFA
Pyruvate kinase

Title: Isotopically nonstationary 13C flux analysis of cyanobacterial isobutyraldehyde production

Citation Formats

References (45)

Cited By (11)

Similar Records

Related Subjects

Title: Isotopically nonstationary ¹³C flux analysis of cyanobacterial isobutyraldehyde production