1
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Flamholz AI, Dugan E, Blikstad C, Gleizer S, Ben-Nissan R, Amram S, Antonovsky N, Ravishankar S, Noor E, Bar-Even A, Milo R, Savage DF. Functional reconstitution of a bacterial CO 2 concentrating mechanism in Escherichia coli. eLife 2020; 9:59882. [PMID: 33084575 PMCID: PMC7714395 DOI: 10.7554/elife.59882] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 10/20/2020] [Indexed: 12/19/2022] Open
Abstract
Many photosynthetic organisms employ a CO2 concentrating mechanism (CCM) to increase the rate of CO2 fixation via the Calvin cycle. CCMs catalyze ≈50% of global photosynthesis, yet it remains unclear which genes and proteins are required to produce this complex adaptation. We describe the construction of a functional CCM in a non-native host, achieved by expressing genes from an autotrophic bacterium in an Escherichia coli strain engineered to depend on rubisco carboxylation for growth. Expression of 20 CCM genes enabled E. coli to grow by fixing CO2 from ambient air into biomass, with growth in ambient air depending on the components of the CCM. Bacterial CCMs are therefore genetically compact and readily transplanted, rationalizing their presence in diverse bacteria. Reconstitution enabled genetic experiments refining our understanding of the CCM, thereby laying the groundwork for deeper study and engineering of the cell biology supporting CO2 assimilation in diverse organisms.
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Affiliation(s)
- Avi I Flamholz
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Eli Dugan
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Cecilia Blikstad
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Shmuel Gleizer
- Department of Plant and Environmental Sciences, Weizmann Institute of ScienceRehovotIsrael
| | - Roee Ben-Nissan
- Department of Plant and Environmental Sciences, Weizmann Institute of ScienceRehovotIsrael
| | - Shira Amram
- Department of Plant and Environmental Sciences, Weizmann Institute of ScienceRehovotIsrael
| | - Niv Antonovsky
- Department of Plant and Environmental Sciences, Weizmann Institute of ScienceRehovotIsrael
| | - Sumedha Ravishankar
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Elad Noor
- Department of Plant and Environmental Sciences, Weizmann Institute of ScienceRehovotIsrael
| | - Arren Bar-Even
- Max Planck Institute of Molecular Plant PhysiologyPotsdamGermany
| | - Ron Milo
- Department of Plant and Environmental Sciences, Weizmann Institute of ScienceRehovotIsrael
| | - David F Savage
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
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2
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Davidi D, Shamshoum M, Guo Z, Bar‐On YM, Prywes N, Oz A, Jablonska J, Flamholz A, Wernick DG, Antonovsky N, de Pins B, Shachar L, Hochhauser D, Peleg Y, Albeck S, Sharon I, Mueller‐Cajar O, Milo R. Highly active rubiscos discovered by systematic interrogation of natural sequence diversity. EMBO J 2020; 39:e104081. [PMID: 32500941 PMCID: PMC7507306 DOI: 10.15252/embj.2019104081] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 04/30/2020] [Accepted: 05/07/2020] [Indexed: 11/09/2022] Open
Abstract
CO2 is converted into biomass almost solely by the enzyme rubisco. The poor carboxylation properties of plant rubiscos have led to efforts that made it the most kinetically characterized enzyme, yet these studies focused on < 5% of its natural diversity. Here, we searched for fast-carboxylating variants by systematically mining genomic and metagenomic data. Approximately 33,000 unique rubisco sequences were identified and clustered into ≈ 1,000 similarity groups. We then synthesized, purified, and biochemically tested the carboxylation rates of 143 representatives, spanning all clusters of form-II and form-II/III rubiscos. Most variants (> 100) were active in vitro, with the fastest having a turnover number of 22 ± 1 s-1 -sixfold faster than the median plant rubisco and nearly twofold faster than the fastest measured rubisco to date. Unlike rubiscos from plants and cyanobacteria, the fastest variants discovered here are homodimers and exhibit a much simpler folding and activation kinetics. Our pipeline can be utilized to explore the kinetic space of other enzymes of interest, allowing us to get a better view of the biosynthetic potential of the biosphere.
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Affiliation(s)
- Dan Davidi
- Department of Plant and Environmental SciencesWeizmann Institute of ScienceRehovotIsrael
- Present address:
Department of GeneticsHarvard Medical SchoolBostonMAUSA
| | - Melina Shamshoum
- Department of Plant and Environmental SciencesWeizmann Institute of ScienceRehovotIsrael
| | - Zhijun Guo
- School of Biological SciencesNanyang Technological UniversitySingaporeSingapore
| | - Yinon M Bar‐On
- Department of Plant and Environmental SciencesWeizmann Institute of ScienceRehovotIsrael
| | - Noam Prywes
- Department of Molecular and Cell BiologyUniversity of CaliforniaBerkeleyCAUSA
| | - Aia Oz
- Migal Galilee Research InstituteKiryat ShmonaIsrael
- Tel Hai CollegeUpper GalileeIsrael
| | - Jagoda Jablonska
- Department of Biomolecular SciencesWeizmann Institute of ScienceRehovotIsrael
| | - Avi Flamholz
- Department of Molecular and Cell BiologyUniversity of CaliforniaBerkeleyCAUSA
| | - David G Wernick
- Department of Plant and Environmental SciencesWeizmann Institute of ScienceRehovotIsrael
- Present address:
BASF Enzymes LLCSan DiegoCAUSA
| | - Niv Antonovsky
- Department of Plant and Environmental SciencesWeizmann Institute of ScienceRehovotIsrael
- Present address:
Laboratory of Genetically Encoded Small MoleculesThe Rockefeller UniversityNew YorkNYUSA
| | - Benoit de Pins
- Department of Plant and Environmental SciencesWeizmann Institute of ScienceRehovotIsrael
| | - Lior Shachar
- Department of Plant and Environmental SciencesWeizmann Institute of ScienceRehovotIsrael
| | - Dina Hochhauser
- Department of Molecular GeneticsWeizmann Institute of ScienceRehovotIsrael
| | - Yoav Peleg
- Department of Life Sciences Core FacilitiesWeizmann Institute of ScienceRehovotIsrael
| | - Shira Albeck
- Department of Life Sciences Core FacilitiesWeizmann Institute of ScienceRehovotIsrael
| | - Itai Sharon
- Migal Galilee Research InstituteKiryat ShmonaIsrael
- Tel Hai CollegeUpper GalileeIsrael
| | | | - Ron Milo
- Department of Plant and Environmental SciencesWeizmann Institute of ScienceRehovotIsrael
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3
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Gleizer S, Ben-Nissan R, Bar-On YM, Antonovsky N, Noor E, Zohar Y, Jona G, Krieger E, Shamshoum M, Bar-Even A, Milo R. Conversion of Escherichia coli to Generate All Biomass Carbon from CO 2. Cell 2020; 179:1255-1263.e12. [PMID: 31778652 PMCID: PMC6904909 DOI: 10.1016/j.cell.2019.11.009] [Citation(s) in RCA: 233] [Impact Index Per Article: 58.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 10/17/2019] [Accepted: 11/04/2019] [Indexed: 01/11/2023]
Abstract
The living world is largely divided into autotrophs that convert CO2 into biomass and heterotrophs that consume organic compounds. In spite of widespread interest in renewable energy storage and more sustainable food production, the engineering of industrially relevant heterotrophic model organisms to use CO2 as their sole carbon source has so far remained an outstanding challenge. Here, we report the achievement of this transformation on laboratory timescales. We constructed and evolved Escherichia coli to produce all its biomass carbon from CO2. Reducing power and energy, but not carbon, are supplied via the one-carbon molecule formate, which can be produced electrochemically. Rubisco and phosphoribulokinase were co-expressed with formate dehydrogenase to enable CO2 fixation and reduction via the Calvin-Benson-Bassham cycle. Autotrophic growth was achieved following several months of continuous laboratory evolution in a chemostat under intensifying organic carbon limitation and confirmed via isotopic labeling.
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Affiliation(s)
- Shmuel Gleizer
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Roee Ben-Nissan
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yinon M Bar-On
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Niv Antonovsky
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Elad Noor
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yehudit Zohar
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ghil Jona
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Eyal Krieger
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Melina Shamshoum
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Arren Bar-Even
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ron Milo
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel.
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4
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Bachar A, Itzhaki E, Gleizer S, Shamshoom M, Milo R, Antonovsky N. Point mutations in topoisomerase I alter the mutation spectrum in E. coli and impact the emergence of drug resistance genotypes. Nucleic Acids Res 2020; 48:761-769. [PMID: 31777935 PMCID: PMC6954433 DOI: 10.1093/nar/gkz1100] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 09/27/2019] [Accepted: 11/21/2019] [Indexed: 11/14/2022] Open
Abstract
Identifying the molecular mechanisms that give rise to genetic variation is essential for the understanding of evolutionary processes. Previously, we have used adaptive laboratory evolution to enable biomass synthesis from CO2 in Escherichia coli. Genetic analysis of adapted clones from two independently evolving populations revealed distinct enrichment for insertion and deletion mutational events. Here, we follow these observations to show that mutations in the gene encoding for DNA topoisomerase I (topA) give rise to mutator phenotypes with characteristic mutational spectra. Using genetic assays and mutation accumulation lines, we find that point mutations in topA increase the rate of sequence deletion and duplication events. Interestingly, we observe that a single residue substitution (R168C) results in a high rate of head-to-tail (tandem) short sequence duplications, which are independent of existing sequence repeats. Finally, we show that the unique mutation spectrum of topA mutants enhances the emergence of antibiotic resistance in comparison to mismatch-repair (mutS) mutators, and leads to new resistance genotypes. Our findings highlight a potential link between the catalytic activity of topoisomerases and the fundamental question regarding the emergence of de novo tandem repeats, which are known modulators of bacterial evolution.
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Affiliation(s)
- Amit Bachar
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Elad Itzhaki
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Shmuel Gleizer
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Melina Shamshoom
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Ron Milo
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Niv Antonovsky
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel.,Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY 10065, USA
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5
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Antonovsky N, Gleizer S, Milo R. Engineering carbon fixation in E. coli : from heterologous RuBisCO expression to the Calvin–Benson–Bassham cycle. Curr Opin Biotechnol 2017; 47:83-91. [DOI: 10.1016/j.copbio.2017.06.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 06/13/2017] [Indexed: 11/26/2022]
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6
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Barenholz U, Davidi D, Reznik E, Bar-On Y, Antonovsky N, Noor E, Milo R. Design principles of autocatalytic cycles constrain enzyme kinetics and force low substrate saturation at flux branch points. eLife 2017; 6. [PMID: 28169831 PMCID: PMC5333975 DOI: 10.7554/elife.20667] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 02/01/2017] [Indexed: 01/01/2023] Open
Abstract
A set of chemical reactions that require a metabolite to synthesize more of that metabolite is an autocatalytic cycle. Here, we show that most of the reactions in the core of central carbon metabolism are part of compact autocatalytic cycles. Such metabolic designs must meet specific conditions to support stable fluxes, hence avoiding depletion of intermediate metabolites. As such, they are subjected to constraints that may seem counter-intuitive: the enzymes of branch reactions out of the cycle must be overexpressed and the affinity of these enzymes to their substrates must be relatively weak. We use recent quantitative proteomics and fluxomics measurements to show that the above conditions hold for functioning cycles in central carbon metabolism of E. coli. This work demonstrates that the topology of a metabolic network can shape kinetic parameters of enzymes and lead to seemingly wasteful enzyme usage. DOI:http://dx.doi.org/10.7554/eLife.20667.001 Many bacteria are able to produce all the molecules they need to survive from a limited supply of nutrients. This allows the bacteria to thrive even in harsh environments where other organisms struggle to live. The bacteria act as miniature chemical factories to convert nutrients into the desired molecules via a series of chemical reactions. Some molecules are made in sets of reactions termed autocatalytic cycles. These reaction sets require a molecule to be present in the cell in order to produce more of that molecule; like how a savings account needs to contain some money before it can generate more via interest. Bacteria have many different enzymes that each drive specific chemical reactions. In order for an autocatalytic cycle to work properly, the cell needs to maintain adequate supplies of the molecule it is trying to make and all of the “intermediate” molecules in the cycle. If less of an intermediate molecule is produced, for example, the cell needs to reduce the demand for that molecule by controlling later chemical reactions in the cycle. Bacteria control chemical reactions by regulating the activities of the enzymes involved, but it is not clear exactly how they regulate the enzymes that drive autocatalytic cycles. Barenholz et al. combined two approaches called proteomics and fluxomics to study autocatalytic cycles in a bacterium known as E. coli. The experiments suggest several core principles allow autocatalytic cycles to work smoothly in the bacteria. The next step is to apply these principles to different kinds of molecules produced in bacterial cells. A future challenge is to search for other structures that regulate chemical reactions in E. coli and other bacteria. Extending our understanding of autocatalytic cycles and other pathways of chemical reactions is essential for designing and engineering new reactions in bacteria. Such knowledge can be used to modify bacteria to produce valuable chemicals in environmentally friendly ways. DOI:http://dx.doi.org/10.7554/eLife.20667.002
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Affiliation(s)
- Uri Barenholz
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Dan Davidi
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Ed Reznik
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States.,Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Yinon Bar-On
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Niv Antonovsky
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Elad Noor
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Ron Milo
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot, Israel
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7
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Antonovsky N, Gleizer S, Noor E, Zohar Y, Herz E, Barenholz U, Zelcbuch L, Amram S, Wides A, Tepper N, Davidi D, Bar-On Y, Bareia T, Wernick DG, Shani I, Malitsky S, Jona G, Bar-Even A, Milo R. Sugar Synthesis from CO2 in Escherichia coli. Cell 2016; 166:115-25. [PMID: 27345370 PMCID: PMC4930481 DOI: 10.1016/j.cell.2016.05.064] [Citation(s) in RCA: 208] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 03/02/2016] [Accepted: 05/17/2016] [Indexed: 11/29/2022]
Abstract
Can a heterotrophic organism be evolved to synthesize biomass from CO2 directly? So far, non-native carbon fixation in which biomass precursors are synthesized solely from CO2 has remained an elusive grand challenge. Here, we demonstrate how a combination of rational metabolic rewiring, recombinant expression, and laboratory evolution has led to the biosynthesis of sugars and other major biomass constituents by a fully functional Calvin-Benson-Bassham (CBB) cycle in E. coli. In the evolved bacteria, carbon fixation is performed via a non-native CBB cycle, while reducing power and energy are obtained by oxidizing a supplied organic compound (e.g., pyruvate). Genome sequencing reveals that mutations in flux branchpoints, connecting the non-native CBB cycle to biosynthetic pathways, are essential for this phenotype. The successful evolution of a non-native carbon fixation pathway, though not yet resulting in net carbon gain, strikingly demonstrates the capacity for rapid trophic-mode evolution of metabolism applicable to biotechnology. PaperClip
Non-native Calvin-Benson cycle allows for sugar synthesis from CO2 in E. coli Metabolic cutoff allows for the decoupling of energy harvesting from biomass synthesis Chemostat-based directed evolution led to the emergence of sugar synthesis from CO2 Mutations in flux branchpoints are essential for the CBB cycle stable operation
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Affiliation(s)
- Niv Antonovsky
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Shmuel Gleizer
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Elad Noor
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yehudit Zohar
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Elad Herz
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Uri Barenholz
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Lior Zelcbuch
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Shira Amram
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Aryeh Wides
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Naama Tepper
- Department of Computer Science, Technion, Israel Institute of Technology, Haifa 3200003, Israel
| | - Dan Davidi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yinon Bar-On
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Tasneem Bareia
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - David G Wernick
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ido Shani
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sergey Malitsky
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ghil Jona
- Department of Biological Services, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Arren Bar-Even
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ron Milo
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel.
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8
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Zelcbuch L, Lindner SN, Zegman Y, Vainberg Slutskin I, Antonovsky N, Gleizer S, Milo R, Bar-Even A. Pyruvate Formate-Lyase Enables Efficient Growth of Escherichia coli on Acetate and Formate. Biochemistry 2016; 55:2423-6. [PMID: 27093333 DOI: 10.1021/acs.biochem.6b00184] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pyruvate formate-lyase (PFL) is a ubiquitous enzyme that supports increased ATP yield during sugar fermentation. While the PFL reaction is known to be reversible in vitro, the ability of PFL to support microbial growth by condensing acetyl-CoA and formate in vivo has never been directly tested. Here, we employ Escherichia coli mutant strains that cannot assimilate acetate via the glyoxylate shunt and use carbon labeling experiments to unequivocally demonstrate PFL-dependent co-assimilation of acetate and formate. Moreover, PFL-dependent growth is faster than growth on acetate using the glyoxylate shunt. Hence, growth via the reverse activity of PFL could have substantial ecological and biotechnological significance.
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Affiliation(s)
- Lior Zelcbuch
- Department of Plant and Environmental Sciences, Weizmann Institute of Science , Rehovot 76100, Israel
| | - Steffen N Lindner
- Max Planck Institute of Molecular Plant Physiology , Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Yonatan Zegman
- Department of Plant and Environmental Sciences, Weizmann Institute of Science , Rehovot 76100, Israel
| | - Ilya Vainberg Slutskin
- Department of Plant and Environmental Sciences, Weizmann Institute of Science , Rehovot 76100, Israel
| | - Niv Antonovsky
- Department of Plant and Environmental Sciences, Weizmann Institute of Science , Rehovot 76100, Israel
| | - Shmuel Gleizer
- Department of Plant and Environmental Sciences, Weizmann Institute of Science , Rehovot 76100, Israel
| | - Ron Milo
- Department of Plant and Environmental Sciences, Weizmann Institute of Science , Rehovot 76100, Israel
| | - Arren Bar-Even
- Max Planck Institute of Molecular Plant Physiology , Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
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9
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Zelcbuch L, Razo-Mejia M, Herz E, Yahav S, Antonovsky N, Kroytoro H, Milo R, Bar-Even A. An in vivo metabolic approach for deciphering the product specificity of glycerate kinase proves that both E. coli's glycerate kinases generate 2-phosphoglycerate. PLoS One 2015; 10:e0122957. [PMID: 25823014 PMCID: PMC4378991 DOI: 10.1371/journal.pone.0122957] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 02/19/2015] [Indexed: 11/18/2022] Open
Abstract
Apart from addressing humanity’s growing demand for fuels, pharmaceuticals, plastics and other value added chemicals, metabolic engineering of microbes can serve as a powerful tool to address questions concerning the characteristics of cellular metabolism. Along these lines, we developed an in vivo metabolic strategy that conclusively identifies the product specificity of glycerate kinase. By deleting E. coli’s phosphoglycerate mutases, we divide its central metabolism into an ‘upper’ and ’lower’ metabolism, each requiring its own carbon source for the bacterium to grow. Glycerate can serve to replace the upper or lower carbon source depending on the product of glycerate kinase. Using this strategy we show that while glycerate kinase from Arabidopsis thaliana produces 3-phosphoglycerate, both E. coli’s enzymes generate 2-phosphoglycerate. This strategy represents a general approach to decipher enzyme specificity under physiological conditions.
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Affiliation(s)
- Lior Zelcbuch
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot Israel
| | - Manuel Razo-Mejia
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot Israel
- Department of Biochemistry and Molecular Biophysics, California Institute of Technology, Pasadena, California, United States of America
| | - Elad Herz
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot Israel
| | - Sagit Yahav
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot Israel
| | - Niv Antonovsky
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot Israel
| | - Hagar Kroytoro
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot Israel
| | - Ron Milo
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot Israel
| | - Arren Bar-Even
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot Israel
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
- * E-mail:
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10
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Levin-Karp A, Barenholz U, Bareia T, Dayagi M, Zelcbuch L, Antonovsky N, Noor E, Milo R. Quantifying translational coupling in E. coli synthetic operons using RBS modulation and fluorescent reporters. ACS Synth Biol 2013; 2:327-36. [PMID: 23654261 DOI: 10.1021/sb400002n] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Translational coupling is the interdependence of translation efficiency of neighboring genes encoded within an operon. The degree of coupling may be quantified by measuring how the translation rate of a gene is modulated by the translation rate of its upstream gene. Translational coupling was observed in prokaryotic operons several decades ago, but the quantitative range of modulation translational coupling leads to and the factors governing this modulation were only partially characterized. In this study, we systematically quantify and characterize translational coupling in E. coli synthetic operons using a library of plasmids carrying fluorescent reporter genes that are controlled by a set of different ribosome binding site (RBS) sequences. The downstream gene expression level is found to be enhanced by the upstream gene expression via translational coupling with the enhancement level varying from almost no coupling to over 10-fold depending on the upstream gene's sequence. Additionally, we find that the level of translational coupling in our system is similar between the second and third locations in the operon. The coupling depends on the distance between the stop codon of the upstream gene and the start codon of the downstream gene. This study is the first to systematically and quantitatively characterize translational coupling in a synthetic E. coli operon. Our analysis will be useful in accurate manipulation of gene expression in synthetic biology and serves as a step toward understanding the mechanisms involved in translational expression modulation.
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Affiliation(s)
- Ayelet Levin-Karp
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Uri Barenholz
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Tasneem Bareia
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Michal Dayagi
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Lior Zelcbuch
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Niv Antonovsky
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Elad Noor
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ron Milo
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
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11
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Fink A, Reuven EM, Arnusch CJ, Shmuel-Galia L, Antonovsky N, Shai Y. Assembly of the TLR2/6 transmembrane domains is essential for activation and is a target for prevention of sepsis. J Immunol 2013; 190:6410-22. [PMID: 23677476 DOI: 10.4049/jimmunol.1202033] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
TLR2, together with TLR1 and TLR6, is essential for detecting lipopeptides and bacterial cell wall components such as lipoteichoic acid from Gram-positive bacteria. In this study, we report that transmembrane domain (TMD)-derived peptides from TLR2 and TLR6 specifically inhibit TLR2 activation. Secretion of the cytokines TNF-α and IL-6 by cultured macrophages (RAW264.7 cell line) was inhibited by these peptides in response to TLR2 activation by lipoteichoic acid (TLR2/6 activator) or palmitoyl (3)-Cys-Ser-Lys(4)-OH (TLR2/1 activator) but not by LPS (TLR4 activator). Extensive biophysical and biochemical assays, combined with GALLEX experiments, show that these peptides heterodimerize with their complementary TMDs on their reciprocal protein. These results suggest that TLR2/6/1 TMD assembly is essential for activating this complex. Importantly, when administered to mice inflicted by TLR2, but not TLR4-driven lethal inflammation, a selected peptide rescued 60% of these septic mice, showing potent in vivo inhibition of TNF-α and IL-6 secretion. Furthermore, this peptide also showed high protection in a whole bacteria model. Owing to the importance of TLR2 regulation under a variety of pathological conditions, compounds that can fine-tune this activity are of great importance.
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Affiliation(s)
- Avner Fink
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
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Zelcbuch L, Antonovsky N, Bar-Even A, Levin-Karp A, Barenholz U, Dayagi M, Liebermeister W, Flamholz A, Noor E, Amram S, Brandis A, Bareia T, Yofe I, Jubran H, Milo R. Spanning high-dimensional expression space using ribosome-binding site combinatorics. Nucleic Acids Res 2013; 41:e98. [PMID: 23470993 PMCID: PMC3643573 DOI: 10.1093/nar/gkt151] [Citation(s) in RCA: 132] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Protein levels are a dominant factor shaping natural and synthetic biological systems. Although proper functioning of metabolic pathways relies on precise control of enzyme levels, the experimental ability to balance the levels of many genes in parallel is a major outstanding challenge. Here, we introduce a rapid and modular method to span the expression space of several proteins in parallel. By combinatorially pairing genes with a compact set of ribosome-binding sites, we modulate protein abundance by several orders of magnitude. We demonstrate our strategy by using a synthetic operon containing fluorescent proteins to span a 3D color space. Using the same approach, we modulate a recombinant carotenoid biosynthesis pathway in Escherichia coli to reveal a diversity of phenotypes, each characterized by a distinct carotenoid accumulation profile. In a single combinatorial assembly, we achieve a yield of the industrially valuable compound astaxanthin 4-fold higher than previously reported. The methodology presented here provides an efficient tool for exploring a high-dimensional expression space to locate desirable phenotypes.
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Affiliation(s)
- Lior Zelcbuch
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
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Shai Y, Cohen T, Cohen SJ, Antonovsky N, Cohen IR. A Similar Motif Shared by HIV-1 gp41 and TCRA Trans-Membrane Domains Exploited by the HIV Virus to Modulate T-Cell Proliferation. Biophys J 2011. [DOI: 10.1016/j.bpj.2010.12.2486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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