Methods and systems for chemoautotrophic production of organic compounds

Fischer, Curt R.; Che, Austin J.; Shetty, Reshma P.; Kelly, Jason R.

Title: Methods and systems for chemoautotrophic production of organic compounds

Abstract

The present disclosure identifies pathways, mechanisms, systems and methods to confer chemoautotrophic production of carbon-based products of interest, such as sugars, alcohols, chemicals, amino acids, polymers, fatty acids and their derivatives, hydrocarbons, isoprenoids, and intermediates thereof, in organisms such that these organisms efficiently convert inorganic carbon to organic carbon-based products of interest using inorganic energy, such as formate, and in particular the use of organisms for the commercial production of various carbon-based products of interest.

Inventors:: Fischer, Curt R.; Che, Austin J.; Shetty, Reshma P.; Kelly, Jason R.

Issue Date:: Tue Jan 08 00:00:00 EST 2013

Research Org.:: DOESC (USDOE Office of Science (SC) (United States))

Sponsoring Org.:: USDOE

OSTI Identifier:: 1082897

Patent Number(s):: 8349587

Application Number:: 13/285,919

Assignee:: Ginkgo BioWorks, Inc. (Boston, MA)

Patent Classifications (CPCs):: C - CHEMISTRY C12 - BIOCHEMISTRY C12N - MICROORGANISMS OR ENZYMES

C - CHEMISTRY C12 - BIOCHEMISTRY C12P - FERMENTATION OR ENZYME-USING PROCESSES TO SYNTHESISE A DESIRED CHEMICAL COMPOUND OR COMPOSITION OR TO SEPARATE OPTICAL ISOMERS FROM A RACEMIC MIXTURE {

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C - CHEMISTRY C12 - BIOCHEMISTRY C12N - MICROORGANISMS OR ENZYMES
C12N15/52 - Genes encoding for enzymes or proenzymes
C12N15/70 - Vectors or expression systems specially adapted for E. coli
C12N9/0006 - {acting on CH-OH groups as donors
C12N9/0051 - {acting on a sulfur group of donors

C - CHEMISTRY C12 - BIOCHEMISTRY C12P - FERMENTATION OR ENZYME-USING PROCESSES TO SYNTHESISE A DESIRED CHEMICAL COMPOUND OR COMPOSITION OR TO SEPARATE OPTICAL ISOMERS FROM A RACEMIC MIXTURE {
C12P5/00 - Preparation of hydrocarbons {or halogenated hydrocarbons}
C12P7/00 - Preparation of oxygen-containing organic compounds
C12P7/16 - Butanols
C12P7/40 - containing a carboxyl group {including Peroxycarboxylic acids

C - CHEMISTRY C12 - BIOCHEMISTRY C12Y - ENZYMES
C12Y101/05006 - Formate dehydrogenase-N
C12Y108/05004 - Sulfide

Y - NEW / CROSS SECTIONAL TECHNOLOGIES Y02 - TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE Y02E - REDUCTION OF GREENHOUSE GAS [GHG] EMISSIONS, RELATED TO ENERGY GENERATION, TRANSMISSION OR DISTRIBUTION
Y02E50/10 - Biofuels

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DOE Contract Number:: AR0000091

Resource Type:: Patent

Country of Publication:: United States

Language:: English

Subject:: 59 BASIC BIOLOGICAL SCIENCES

Citation Formats


                    Fischer, Curt R., Che, Austin J., Shetty, Reshma P., and Kelly, Jason R. Methods and systems for chemoautotrophic production of organic compounds.  United States: N. p., 2013. 
        Web.

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                    Fischer, Curt R., Che, Austin J., Shetty, Reshma P., & Kelly, Jason R. Methods and systems for chemoautotrophic production of organic compounds.  United States.

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                    Fischer, Curt R., Che, Austin J., Shetty, Reshma P., and Kelly, Jason R. Tue .  
        "Methods and systems for chemoautotrophic production of organic compounds".  United States.  https://www.osti.gov/servlets/purl/1082897.

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@article{osti_1082897,

  title        = {Methods and systems for chemoautotrophic production of organic compounds},

  author       = {Fischer, Curt R. and Che, Austin J. and Shetty, Reshma P. and Kelly, Jason R.},

  abstractNote = {The present disclosure identifies pathways, mechanisms, systems and methods to confer chemoautotrophic production of carbon-based products of interest, such as sugars, alcohols, chemicals, amino acids, polymers, fatty acids and their derivatives, hydrocarbons, isoprenoids, and intermediates thereof, in organisms such that these organisms efficiently convert inorganic carbon to organic carbon-based products of interest using inorganic energy, such as formate, and in particular the use of organisms for the commercial production of various carbon-based products of interest.},

  doi          = {},

  journal      = {},
number       = ,

  volume       = ,

  place        = {United States},

  year         = {Tue Jan 08 00:00:00 EST 2013},

  month        = {Tue Jan 08 00:00:00 EST 2013}

}

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Title: Methods and systems for chemoautotrophic production of organic compounds

Abstract

Citation Formats

Controls on the stable isotope composition of seasonal growth bands in aragonitic fresh-water bivalves (unionidae) journal, April 1999

Pathways of Carbon and Energy Metabolism of the Epibiotic Community Associated with the Deep-Sea Hydrothermal Vent Shrimp Rimicaris exoculata journal, January 2011

Engineering a non-native hydrogen production pathway into Escherichia coli via a cyanobacterial [NiFe] hydrogenase journal, July 2011

A single mutation in the NAD-specific formate dehydrogenase from Candida methylica allows the enzyme to use NADP journal, January 2001

The FabR (YijC) Transcription Factor Regulates Unsaturated Fatty Acid Biosynthesis in Escherichia coli journal, February 2002

Nautilia lithotrophica gen. nov., sp. nov., a thermophilic sulfur-reducing epsilon-proteobacterium isolated from a deep-sea hydrothermal vent journal, July 2002

Molecular Biology of Microbial Hydrogenases journal, January 2004

Alkane biosynthesis by decarbonylation of aldehyde catalyzed by a microsomal preparation from Botryococcus braunii journal, June 1991

Production of biohydrogen by heterologous expression of oxygen-tolerant Hydrogenovibrio marinus [NiFe]-hydrogenase in Escherichia coli journal, September 2011

Predicting specificity in bZIP coiled-coil protein interactions journal, January 2004

Codon catalog usage and the genome hypothesis journal, January 1980

Microdiesel: Escherichia coli engineered for fuel production journal, September 2006

The National Center for Biotechnology Information's Protein Clusters Database journal, October 2008

The Archaeon Pyrococcus horikoshii Possesses a Bifunctional Enzyme for Formaldehyde Fixation via the Ribulose Monophosphate Pathway journal, May 2005

Identification of a cyclohexylcarbonyl CoA biosynthetic gene cluster and application in the production of doramectin journal, September 2000

A second branched-chain alpha-keto acid dehydrogenase gene cluster (bkdFGH) from Streptomyces avermitilis: its relationship to avermectin biosynthesis and the construction of a bkdF mutant suitable for the production of novel antiparasitic avermectins. journal, June 1995

A novel NADP+-dependent formate dehydrogenase from Burkholderia stabilis 15516: Screening, purification and characterization journal, June 2010

Thermal regulation of membrane fluidity in Escherichia coli. Effects of overproduction of beta-ketoacyl-acyl carrier protein synthase I. journal, February 1983

Directed evolution of RuBisCO hypermorphs through genetic selection in engineered E.coli journal, January 2006

MUSCLE: multiple sequence alignment with high accuracy and high throughput journal, March 2004

A Novel Δ3,Δ2-Enoyl-CoA Isomerase Involved in the Biosynthesis of the Cyclohexanecarboxylic Acid-Derived Moiety of the Polyketide Ansatrienin A journal, June 2000

Solubility of Proteins Isolated from Inclusion Bodies Is Enhanced by Fusion to Maltose-Binding Protein or Thioredoxin journal, February 1998

Synthesis of Methyl Halides from Biomass Using Engineered Microbes journal, May 2009

Chloroflexus aurantiacus secretes 3-hydroxypropionate, a possible intermediate in the assimilation of CO2 and acetate journal, February 1989

Metabolic gene–deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes journal, September 2004

Expression and assembly of active cyanobacterial ribulose-1,5-bisphosphate carboxylase/oxygenase in Escherichia coli containing stoichiometric amounts of large and small subunits. journal, September 1985

Alkane biosynthesis by decarbonylation of aldehydes catalyzed by a particulate preparation from Pisum sativum. journal, November 1984

Metabolic Deficiences Revealed in the Biotechnologically Important Model Bacterium Escherichia coli BL21(DE3) journal, August 2011

Dependence of biodiesel fuel properties on the structure of fatty acid alkyl esters journal, June 2005

A novel biotin protein required for reductive carboxylation of 2-oxoglutarate by isocitrate dehydrogenase in Hydrogenobacter thermophilus TK-6 journal, December 2003

A novel enzyme, citryl-CoA synthetase, catalysing the first step of the citrate cleavage reaction in Hydrogenobacter thermophilus TK-6 journal, March 2004

A Bicyclic Autotrophic CO2 Fixation Pathway in Chloroflexus aurantiacus journal, April 2002

A novel alternate anaplerotic pathway to the glyoxylate cycle in streptomycetes. journal, August 1997

Microbiology of synthesis gas fermentation for biofuel production journal, June 2007

Limitations and prospects of natural photosynthesis for bioenergy production journal, June 2010

Comparison of methods to determine algal δ 13 C in freshwater: Algal δ 13 C in freshwater journal, January 2008

Propionyl-Coenzyme A Synthase from Chloroflexus aurantiacus, a Key Enzyme of the 3-Hydroxypropionate Cycle for Autotrophic CO2 Fixation journal, January 2002

Purification and Properties of α-Ketoglutarate Synthase from a Photosynthetic Bacterium journal, November 1972

Installation of genomes or partial genomes into cells or cell-like systems patent-application, November 2007

Adaptations to Submarine Hydrothermal Environments Exemplified by the Genome of Nautilia profundicola journal, February 2009

Malonyl-Coenzyme A Reductase from Chloroflexus aurantiacus, a Key Enzyme of the 3-Hydroxypropionate Cycle for Autotrophic CO2 Fixation journal, May 2002

The Effect of NAPRTase Overexpression on the Total Levels of NAD, The NADH/NAD+ Ratio, and the Distribution of Metabolites in Escherichia coli journal, July 2002

Improved NADPH supply for xylitol production by engineered Escherichia coli with glycolytic mutations journal, February 2011

Occurrence, Classification, and Biological Function of Hydrogenases: An Overview journal, October 2007

Metabolic Impact of Increased NADH Availability in Saccharomyces cerevisiae journal, December 2009

Biodiesel: The Use of Vegetable Oils and Their Derivatives as Alternative Diesel Fuels book, May 1997

Alteration of the Fatty Acid Profile of Streptomyces coelicolor by Replacement of the Initiation Enzyme 3-Ketoacyl Acyl Carrier Protein Synthase III (FabH) journal, May 2005

Conversion Of Natural Products Including Cellulose To Hydrocarbons, Hydrogen And/Or Other Related Compounds patent-application, September 2010

Sulfide oxidation in gram-negative bacteria by expression of the sulfide–quinone reductase gene of Rhodobacter capsulatus and by electron transport to ubiquinone journal, January 2001

Characterization of enzymes involved in the ethanol production of Moorella sp. HUC22-1 journal, February 2007

GlcP constitutes the major glucose uptake system of Streptomyces coelicolor A3(2) journal, December 2004

Bifunctional enzyme fusion of 3-hexulose-6-phosphate synthase and 6-phospho-3-hexuloisomerase journal, May 2007

Determination of saponifiable glycerol in “Bio-Diesel” journal, March 1991

Directed evolution of proteins by exon shuffling journal, May 2001

Nautilia profundicola sp. nov., a thermophilic, sulfur-reducing epsilonproteobacterium from deep-sea hydrothermal vents journal, July 2008

Purification and properties of 3-hexulose phosphate synthase and phospho-3-hexuloisomerase from Methylococcus capsulatus journal, December 1974

Molecular and genetical analysis of the fructose-glucose transport system in the cyanobacterium Synechocystis PCC6803 journal, September 1989

A new structure-based classification of sulfide:quinone oxidoreductases journal, December 2009

Side effects of chaperone gene co-expression in recombinant protein production journal, January 2010

Engineering BioBrick vectors from BioBrick parts journal, January 2008

Estimation of Nitrogenase Using a Colorimetric Determination for Ethylene journal, June 1973

Autotrophic CO2 fixation via the reductive tricarboxylic acid cycle in different lineages within the phylum Aquificae: evidence for two ways of citrate cleavage journal, January 2007

Nalidixic Acid-Resistant Mutants of Escherichia coli Deficient in Isocitrate Dehydrogenase journal, January 1971

The COG database: an updated version includes eukaryotes journal, January 2003

The Path of Carbon in Photosynthesis. XXI. The Cyclic Regeneration of Carbon Dioxide Acceptor 1 journal, April 1954

Characterization of isocitrate dehydrogenase from the green sulfur bacterium Chlorobium limicola: A carbon dioxide-fixing enzyme in the reductive tricarboxylic acid cycle journal, April 2002

The Soluble and Membrane-bound Transhydrogenases UdhA and PntAB Have Divergent Functions in NADPH Metabolism of Escherichia coli journal, December 2003

The L-Tartrate/Succinate Antiporter TtdT (YgjE) of L-Tartrate Fermentation in Escherichia coli journal, December 2006

Properties of R-Citramalyl-Coenzyme A Lyase and Its Role in the Autotrophic 3-Hydroxypropionate Cycle of Chloroflexus aurantiacus journal, January 2007

Knowledge discovery in gene-expression-microarray data: mining the information output of the genome journal, November 1999

Genome-Scale Thermodynamic Analysis of Escherichia coli Metabolism journal, February 2006

Bacterial Small-Molecule Signaling Pathways journal, February 2006

Increased unsaturated fatty acid production associated with a suppressor of the fabA6(Ts) mutation in Escherichia coli. journal, September 1996

A reverse KREBS cycle in photosynthesis: consensus at last journal, April 1990

Retrobiosynthetic analysis of carbon fixation in the phototrophic eubacterium Chloroflexus aurantiacus journal, August 1993

Protein evolution by molecular breeding journal, June 1999

The carbon assimilation pathways of Methylococcus capsulatus, Pseudomonas methanica and Methylosinus trichosporium (OB3B) during growth on methane journal, December 1974

Controls on the stable isotope composition of seasonal growth bands in aragonitic fresh-water bivalves (unionidae)
journal, April 1999

Pathways of Carbon and Energy Metabolism of the Epibiotic Community Associated with the Deep-Sea Hydrothermal Vent Shrimp Rimicaris exoculata
journal, January 2011

Engineering a non-native hydrogen production pathway into Escherichia coli via a cyanobacterial [NiFe] hydrogenase
journal, July 2011

A single mutation in the NAD-specific formate dehydrogenase from Candida methylica allows the enzyme to use NADP
journal, January 2001

The FabR (YijC) Transcription Factor Regulates Unsaturated Fatty Acid Biosynthesis in Escherichia coli
journal, February 2002

Nautilia lithotrophica gen. nov., sp. nov., a thermophilic sulfur-reducing epsilon-proteobacterium isolated from a deep-sea hydrothermal vent
journal, July 2002

Molecular Biology of Microbial Hydrogenases
journal, January 2004

Alkane biosynthesis by decarbonylation of aldehyde catalyzed by a microsomal preparation from Botryococcus braunii
journal, June 1991

Production of biohydrogen by heterologous expression of oxygen-tolerant Hydrogenovibrio marinus [NiFe]-hydrogenase in Escherichia coli
journal, September 2011

Predicting specificity in bZIP coiled-coil protein interactions
journal, January 2004

Codon catalog usage and the genome hypothesis
journal, January 1980

Microdiesel: Escherichia coli engineered for fuel production
journal, September 2006

The National Center for Biotechnology Information's Protein Clusters Database
journal, October 2008

The Archaeon Pyrococcus horikoshii Possesses a Bifunctional Enzyme for Formaldehyde Fixation via the Ribulose Monophosphate Pathway
journal, May 2005

Identification of a cyclohexylcarbonyl CoA biosynthetic gene cluster and application in the production of doramectin
journal, September 2000

A second branched-chain alpha-keto acid dehydrogenase gene cluster (bkdFGH) from Streptomyces avermitilis: its relationship to avermectin biosynthesis and the construction of a bkdF mutant suitable for the production of novel antiparasitic avermectins.
journal, June 1995

A novel NADP⁺-dependent formate dehydrogenase from Burkholderia stabilis 15516: Screening, purification and characterization
journal, June 2010

Thermal regulation of membrane fluidity in Escherichia coli. Effects of overproduction of beta-ketoacyl-acyl carrier protein synthase I.
journal, February 1983

Directed evolution of RuBisCO hypermorphs through genetic selection in engineered E.coli
journal, January 2006

MUSCLE: multiple sequence alignment with high accuracy and high throughput
journal, March 2004

A Novel Δ³,Δ²-Enoyl-CoA Isomerase Involved in the Biosynthesis of the Cyclohexanecarboxylic Acid-Derived Moiety of the Polyketide Ansatrienin A
journal, June 2000

Solubility of Proteins Isolated from Inclusion Bodies Is Enhanced by Fusion to Maltose-Binding Protein or Thioredoxin
journal, February 1998

Synthesis of Methyl Halides from Biomass Using Engineered Microbes
journal, May 2009

Chloroflexus aurantiacus secretes 3-hydroxypropionate, a possible intermediate in the assimilation of CO₂ and acetate
journal, February 1989

Metabolic gene–deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes
journal, September 2004

Expression and assembly of active cyanobacterial ribulose-1,5-bisphosphate carboxylase/oxygenase in Escherichia coli containing stoichiometric amounts of large and small subunits.
journal, September 1985

Alkane biosynthesis by decarbonylation of aldehydes catalyzed by a particulate preparation from Pisum sativum.
journal, November 1984

Metabolic Deficiences Revealed in the Biotechnologically Important Model Bacterium Escherichia coli BL21(DE3)
journal, August 2011

Dependence of biodiesel fuel properties on the structure of fatty acid alkyl esters
journal, June 2005

A novel biotin protein required for reductive carboxylation of 2-oxoglutarate by isocitrate dehydrogenase in Hydrogenobacter thermophilus TK-6
journal, December 2003

A novel enzyme, citryl-CoA synthetase, catalysing the first step of the citrate cleavage reaction in Hydrogenobacter thermophilus TK-6
journal, March 2004

A Bicyclic Autotrophic CO₂ Fixation Pathway in Chloroflexus aurantiacus
journal, April 2002

A novel alternate anaplerotic pathway to the glyoxylate cycle in streptomycetes.
journal, August 1997

Microbiology of synthesis gas fermentation for biofuel production
journal, June 2007

Limitations and prospects of natural photosynthesis for bioenergy production
journal, June 2010

Comparison of methods to determine algal δ ¹³ C in freshwater: Algal δ ¹³ C in freshwater
journal, January 2008

Propionyl-Coenzyme A Synthase from Chloroflexus aurantiacus, a Key Enzyme of the 3-Hydroxypropionate Cycle for Autotrophic CO₂ Fixation
journal, January 2002

Purification and Properties of α-Ketoglutarate Synthase from a Photosynthetic Bacterium
journal, November 1972

Installation of genomes or partial genomes into cells or cell-like systems
patent-application, November 2007

Adaptations to Submarine Hydrothermal Environments Exemplified by the Genome of Nautilia profundicola
journal, February 2009

Malonyl-Coenzyme A Reductase from Chloroflexus aurantiacus, a Key Enzyme of the 3-Hydroxypropionate Cycle for Autotrophic CO₂ Fixation
journal, May 2002

The Effect of NAPRTase Overexpression on the Total Levels of NAD, The NADH/NAD⁺ Ratio, and the Distribution of Metabolites in Escherichia coli
journal, July 2002

Improved NADPH supply for xylitol production by engineered Escherichia coli with glycolytic mutations
journal, February 2011

Occurrence, Classification, and Biological Function of Hydrogenases: An Overview
journal, October 2007

Metabolic Impact of Increased NADH Availability in Saccharomyces cerevisiae
journal, December 2009

Biodiesel: The Use of Vegetable Oils and Their Derivatives as Alternative Diesel Fuels
book, May 1997

Alteration of the Fatty Acid Profile of Streptomyces coelicolor by Replacement of the Initiation Enzyme 3-Ketoacyl Acyl Carrier Protein Synthase III (FabH)
journal, May 2005

Conversion Of Natural Products Including Cellulose To Hydrocarbons, Hydrogen And/Or Other Related Compounds
patent-application, September 2010

Sulfide oxidation in gram-negative bacteria by expression of the sulfide–quinone reductase gene of Rhodobacter capsulatus and by electron transport to ubiquinone
journal, January 2001

Characterization of enzymes involved in the ethanol production of Moorella sp. HUC22-1
journal, February 2007

GlcP constitutes the major glucose uptake system of Streptomyces coelicolor A3(2)
journal, December 2004

Bifunctional enzyme fusion of 3-hexulose-6-phosphate synthase and 6-phospho-3-hexuloisomerase
journal, May 2007

Determination of saponifiable glycerol in “Bio-Diesel”
journal, March 1991

Directed evolution of proteins by exon shuffling
journal, May 2001

Nautilia profundicola sp. nov., a thermophilic, sulfur-reducing epsilonproteobacterium from deep-sea hydrothermal vents
journal, July 2008

Purification and properties of 3-hexulose phosphate synthase and phospho-3-hexuloisomerase from Methylococcus capsulatus
journal, December 1974

Molecular and genetical analysis of the fructose-glucose transport system in the cyanobacterium Synechocystis PCC6803
journal, September 1989

A new structure-based classification of sulfide:quinone oxidoreductases
journal, December 2009

Side effects of chaperone gene co-expression in recombinant protein production
journal, January 2010

Engineering BioBrick vectors from BioBrick parts
journal, January 2008

Estimation of Nitrogenase Using a Colorimetric Determination for Ethylene
journal, June 1973

Autotrophic CO₂ fixation via the reductive tricarboxylic acid cycle in different lineages within the phylum Aquificae: evidence for two ways of citrate cleavage
journal, January 2007

Nalidixic Acid-Resistant Mutants of Escherichia coli Deficient in Isocitrate Dehydrogenase
journal, January 1971

The COG database: an updated version includes eukaryotes
journal, January 2003

The Path of Carbon in Photosynthesis. XXI. The Cyclic Regeneration of Carbon Dioxide Acceptor ¹
journal, April 1954

Characterization of isocitrate dehydrogenase from the green sulfur bacterium Chlorobium limicola: A carbon dioxide-fixing enzyme in the reductive tricarboxylic acid cycle
journal, April 2002

The Soluble and Membrane-bound Transhydrogenases UdhA and PntAB Have Divergent Functions in NADPH Metabolism of Escherichia coli
journal, December 2003

The L-Tartrate/Succinate Antiporter TtdT (YgjE) of L-Tartrate Fermentation in Escherichia coli
journal, December 2006

Properties of R-Citramalyl-Coenzyme A Lyase and Its Role in the Autotrophic 3-Hydroxypropionate Cycle of Chloroflexus aurantiacus
journal, January 2007

Knowledge discovery in gene-expression-microarray data: mining the information output of the genome
journal, November 1999

Genome-Scale Thermodynamic Analysis of Escherichia coli Metabolism
journal, February 2006

Bacterial Small-Molecule Signaling Pathways
journal, February 2006

Increased unsaturated fatty acid production associated with a suppressor of the fabA6(Ts) mutation in Escherichia coli.
journal, September 1996

A reverse KREBS cycle in photosynthesis: consensus at last
journal, April 1990

Retrobiosynthetic analysis of carbon fixation in the phototrophic eubacterium Chloroflexus aurantiacus
journal, August 1993

Protein evolution by molecular breeding
journal, June 1999

The carbon assimilation pathways of Methylococcus capsulatus, Pseudomonas methanica and Methylosinus trichosporium (OB3B) during growth on methane
journal, December 1974

Production of 3-hydroxypropionic acid via malonyl-CoA pathway using recombinant Escherichia coli strains
journal, February 2012

Overexpression in Escherichia coli of 12 Vitamin B₁₂ Biosynthetic Enzymes
journal, April 1995

Malonyl-Coenzyme A Reductase in the Modified 3-Hydroxypropionate Cycle for Autotrophic Carbon Fixation in Archaeal Metallosphaera and Sulfolobus spp.
journal, October 2006