Awakening a latent carbon fixation cycle in Escherichia coli

Nature Communications
A. SatanowskiArren Bar-Even

Abstract

Carbon fixation is one of the most important biochemical processes. Most natural carbon fixation pathways are thought to have emerged from enzymes that originally performed other metabolic tasks. Can we recreate the emergence of a carbon fixation pathway in a heterotrophic host by recruiting only endogenous enzymes? In this study, we address this question by systematically analyzing possible carbon fixation pathways composed only of Escherichia coli native enzymes. We identify the GED (Gnd-Entner-Doudoroff) cycle as the simplest pathway that can operate with high thermodynamic driving force. This autocatalytic route is based on reductive carboxylation of ribulose 5-phosphate (Ru5P) by 6-phosphogluconate dehydrogenase (Gnd), followed by reactions of the Entner-Doudoroff pathway, gluconeogenesis, and the pentose phosphate pathway. We demonstrate the in vivo feasibility of this new-to-nature pathway by constructing E. coli gene deletion strains whose growth on pentose sugars depends on the GED shunt, a linear variant of the GED cycle which does not require the regeneration of Ru5P. Several metabolic adaptations, most importantly the increased production of NADPH, assist in establishing sufficiently high flux to sustain this growth...Continue Reading

References

Jan 1, 1975·Methods in Enzymology·M Silverberg, K Dalziel
Feb 15, 1992·Proceedings of the National Academy of Sciences of the United States of America·K Schnetz, B Rak
May 13, 1982·Nature·M Kröger, G Hobom
Dec 11, 1999·Nucleic Acids Research·M Kanehisa, S Goto
Jun 1, 2000·Proceedings of the National Academy of Sciences of the United States of America·K A Datsenko, B L Wanner
Feb 16, 2002·Methods : a Companion to Methods in Enzymology·K J Livak, T D Schmittgen
Jun 7, 2005·Biochimica Et Biophysica Acta·Tania BizouarnJ Baz Jackson
Jun 2, 2006·Molecular Systems Biology·Koji HayashiTakashi Horiuchi
Jun 14, 2006·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Masanari KitagawaHirotada Mori
Jun 6, 2007·Proceedings of the National Academy of Sciences of the United States of America·Tobias J ErbBirgit E Alber
Dec 25, 2007·Journal of Biology·Markus RalserSylvia Krobitsch
Jun 13, 2008·Nature Protocols·Thomas D Schmittgen, Kenneth J Livak
Oct 17, 2009·PLoS Genetics·Zhongge Zhang, Milton H Saier
Apr 23, 2010·Proceedings of the National Academy of Sciences of the United States of America·Arren Bar-EvenRon Milo
May 11, 2010·The Journal of Biological Chemistry·Stefania HanauFranco Dallocchio
Dec 7, 2010·Applied and Environmental Microbiology·Rintze M ZelleAntonius J A van Maris
Jan 11, 2011·Applied and Environmental Microbiology·Ivan A Berg
Feb 19, 2011·Annual Review of Marine Science·Michael Hügler, Stefan M Sievert
Nov 9, 2011·Nucleic Acids Research·Avi FlamholzRon Milo
Dec 28, 2011·Journal of Experimental Botany·Arren Bar-EvenRon Milo
Apr 27, 2012·PLoS Computational Biology·Rogier Braakman, Eric Smith
Mar 9, 2013·Nucleic Acids Research·Lior ZelcbuchRon Milo
Aug 10, 2013·BMC Systems Biology·Ali EbrahimDaniel R Hyduke
Aug 31, 2013·Biotechnology for Biofuels·Víctor Guadalupe-MedinaAntonius Ja van Maris
Oct 25, 2013·Bioresource Technology·Zong-Yu Zhuang, Si-Yu Li
Mar 4, 2014·PLoS Computational Biology·Elad NoorRon Milo
Jul 8, 2015·Antonie van Leeuwenhoek·Danilo J P RochaLuis G C Pacheco
May 12, 2016·Proceedings of the National Academy of Sciences of the United States of America·Luke C M MackinderMartin C Jonikas
Jun 28, 2016·Cell·Niv AntonovskyRon Milo

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Citations

Feb 6, 2021·Trends in Biotechnology·Mihris Ibnu Saleem NaduthodiMaria J Barbosa
Feb 2, 2021·Trends in Biotechnology·Justin PanichSteven W Singer
May 10, 2021·Trends in Biotechnology·Li ZhuSheng Yang
Jul 19, 2021·Microbiological Research·Ayesha NisarSardar Azhar Mehmood
Jul 28, 2021·Nature Chemical Biology·Wei JiangRodrigo Ledesma-Amaro
Aug 4, 2021·Nature Reviews. Microbiology·José Montaño LópezJosé L Avalos
Sep 8, 2021·Nature Communications·Enrico OrsiSteffen N Lindner

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Datasets Mentioned

BETA
MW059023
MG1655

Methods Mentioned

BETA
PCR
electrophoresis

Software Mentioned

AnnoTree
Geneious
COBRApy
iTOL

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