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Title: Methods and systems for chemoautotrophic production of organic compounds


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.

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Issue Date:
Research Org.:
Ginkgo BioWorks, Inc., Boston, MA (United States)
Sponsoring Org.:
OSTI Identifier:
Patent Number(s):
Application Number:
Ginkgo BioWorks, Inc. (Boston, MA)
DOE Contract Number:  
Resource Type:
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Patent File Date: 2012 Oct 30
Country of Publication:
United States

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., 2018. Web.
Fischer, Curt R., Che, Austin J., Shetty, Reshma P., & Kelly, Jason R. Methods and systems for chemoautotrophic production of organic compounds. United States.
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.
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 = {2018},
month = {2}


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Works referenced in this record:

Synthetic genomes
patent-application, November 2007

Novel Enzyme
patent-application, April 2010

Developments in Directed Evolution for Improving Enzyme Functions
journal, August 2007

  • Sen, S.; Venkata Dasu, V.; Mandal, B.
  • Applied Biochemistry and Biotechnology, Vol. 143, Issue 3, p. 212-223
  • DOI: 10.1007/s12010-007-8003-4

Semi-rational approaches to engineering enzyme activity: combining the benefits of directed evolution and rational design
journal, August 2005

  • Chica, Roberto A.; Doucet, Nicolas; Pelletier, Joelle N.
  • Current Opinion in Biotechnology, Vol. 16, Issue 4, p. 378-384
  • DOI: 10.1016/j.copbio.2005.06.004

Prediction of protein function from protein sequence and structure
journal, January 1999

  • Whisstock, James C.; Lesk, Arthur M.
  • Quarterly Reviews of Biophysics, Vol. 36, Issue 3, p. 307-340
  • DOI: 10.1017/S0033583503003901

Ensemble modeling for strain development of l-lysine-producing Escherichia coli
journal, July 2009

  • Contador, Carolina A.; Rizk, Matthew L.; Asenjo, Juan A.
  • Metabolic Engineering, Vol. 11, Issue 4-5, p. 221-233
  • DOI: 10.1016/j.ymben.2009.04.002

The ribulose monophosphate pathway operon encoding formaldehyde fixation in a thermotolerant methylotroph, Bacillus brevis S1
journal, September 2002

Assessment of heterologous butyrate and butanol pathway activity by measurement of intracellular pathway intermediates in recombinant Escherichia coli
journal, July 2010

  • Fischer, Curt R.; Tseng, Hsien-Chung; Tai, Mitchell
  • Applied Microbiology and Biotechnology, Vol. 88, Issue 1, p. 265-275
  • DOI: 10.1007/s00253-010-2749-2

Carbon Isotope Fractionation In Formation Of Amino Acids By Photosynthetic Organisms
journal, May 1961

  • Abelson, P. H.; Hoering, T. C.
  • Proceedings of the National Academy of Sciences, Vol. 47, Issue 5, p. 623-632
  • DOI: 10.1073/pnas.47.5.623

An algorithm for operating a fed-batch fermentor at optimum specific-growth rate
journal, January 1989

  • Agrawal, Pramod; Koshy, George; Ramseier, Michael
  • Biotechnology and Bioengineering, Vol. 33, Issue 1, p. 115-125
  • DOI: 10.1002/bit.260330115

Identification of the SAAT Gene Involved in Strawberry Flavor Biogenesis by Use of DNA Microarrays
journal, May 2000

  • Aharoni, Asaph; Keizer, Leopold C. P.; Bouwmeester, Harro J.
  • The Plant Cell, Vol. 12, Issue 5, p. 647-662
  • DOI: 10.1105/tpc.12.5.647

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

  • Alber, B.; Olinger, M.; Rieder, A.
  • Journal of Bacteriology, Vol. 188, Issue 24, p. 8551-8559
  • DOI: 10.1128/JB.00987-06

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

  • Alber, Birgit E.; Fuchs, Georg
  • Journal of Biological Chemistry, Vol. 277, Issue 14, p. 12137-12143
  • DOI: 10.1074/jbc.M110802200

Environmental signal integration by a modular AND gate
journal, August 2007

  • Anderson, J. Christopher; Voigt, Christopher A.; Arkin, Adam P.
  • Molecular Systems Biology, Vol. 3, Issue 1, Article No. 133
  • DOI: 10.1038/msb4100173

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 lyase, catalysing the second step of the citrate cleavage reaction in Hydrogenobacter thermophilus TK-6
journal, March 2004

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

A novel oxalosuccinate-forming enzyme involved in the reductive carboxylation of 2-oxoglutarate in Hydrogenobacter thermophilus TK-6
journal, November 2006

Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants the Keio collection
journal, February 2006

  • Baba, Tomoya; Ara, Takeshi; Hasegawa, Miki
  • Molecular Systems Biology, Vol. 2, Article No. 2006.0008
  • DOI: 10.1038/msb4100050

Ethanol fermentation technologies from sugar and starch feedstocks
journal, January 2008

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

  • Bailer, Josef; de Hueber, Karl
  • Fresenius' Journal of Analytical Chemistry, Vol. 340, Issue 3, p. 186-186
  • DOI: 10.1007/BF00324480

Design and analysis of synthetic carbon fixation pathways
journal, April 2010

  • Bar-Even, A.; Noor, E.; Lewis, N. E.
  • Proceedings of the National Academy of Sciences, Vol. 107, Issue 19, p. 8889-8894
  • DOI: 10.1073/pnas.0907176107

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

  • Bayer, Travis S.; Widmaier, Daniel M.; Temme, Karsten
  • Journal of the American Chemical Society, Vol. 131, Issue 18, p. 6508-6515
  • DOI: 10.1021/ja809461u

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

  • Berríos-Rivera, Susana J.; San, K.-Y.; Bennett, G. N.
  • Metabolic Engineering, Vol. 4, Issue 3, p. 238-247
  • DOI: 10.1006/mben.2002.0229

High-cell-density production of poly-β-hydroxybutyrate (PHB) from methanol by Methylobacterium extorquens: production of high-molecular-mass PHB
journal, December 1995

  • Bourque, D.; Pomerleau, Y.; Groleau, D.
  • Applied Microbiology and Biotechnology, Vol. 44, Issue 3-4, p. 367-376
  • DOI: 10.1007/BF00169931

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

  • Buchanan, Bob B.; Arnon, Daniel I.
  • Photosynthesis Research, Vol. 24, Issue 1, p. 47-53
  • DOI: 10.1007/BF00032643

The Soluble NAD+-Reducing [NiFe]-Hydrogenase from Ralstonia eutropha H16 Consists of Six Subunits and Can Be Specifically Activated by NADPH
journal, April 2005

Bacterial Small-Molecule Signaling Pathways
journal, February 2006

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

  • Campbell, Barbara J.; Smith, Julie L.; Hanson, Thomas E.
  • PLoS Genetics, Vol. 5, Issue 2, Article No. e1000362
  • DOI: 10.1371/journal.pgen.1000362

Growth and Phylogenetic Properties of Novel Bacteria Belonging to the Epsilon Subdivision of the Proteobacteria Enriched from Alvinella pompejana and Deep-Sea Hydrothermal Vents
journal, October 2001

Refinement and standardization of synthetic biological parts and devices
journal, July 2008

  • Canton, Barry; Labno, Anna; Endy, Drew
  • Nature Biotechnology, Vol. 26, Issue 7, p. 787-793
  • DOI: 10.1038/nbt1413

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

  • Cheesbrough, T. M.; Kolattukudy, P. E.
  • Proceedings of the National Academy of Sciences, Vol. 81, Issue 21, p. 6613-6617
  • DOI: 10.1073/pnas.81.21.6613

Biosynthesis of ansatrienin (mycotrienin) and naphthomycin. Identification and analysis of two separate biosynthetic gene clusters in Streptomyces collinus Tu 1892
journal, March 1999

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

  • Chin, Jonathan W.; Cirino, Patrick C.
  • Biotechnology Progress, Vol. 27, Issue 2, p. 333-341
  • DOI: 10.1002/btpr.559

Spectrophotometric Determination Of Hydrogen Sulfide In Natural Waters
journal, May 1969

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

  • Cropp, T. Ashton; Wilson, Dennis J.; Reynolds, K. A.
  • Nature Biotechnology, Vol. 18, Issue 9, p. 980-983
  • DOI: 10.1038/79479

Formate as the Main Branch Point for Methylotrophic Metabolism in Methylobacterium extorquens AM1
journal, May 2008

  • Crowther, G. J.; Kosaly, G.; Lidstrom, M. E.
  • Journal of Bacteriology, Vol. 190, Issue 14, p. 5057-5062
  • DOI: 10.1128/JB.00228-08

Design, construction and characterization of a set of insulated bacterial promoters
journal, September 2010

  • Davis, J. H.; Rubin, A. J.; Sauer, R. T.
  • Nucleic Acids Research, Vol. 39, Issue 3, p. 1131-1141
  • DOI: 10.1093/nar/gkq810

Engineered reversal of the β-oxidation cycle for the synthesis of fuels and chemicals
journal, August 2011

  • Dellomonaco, Clementina; Clomburg, James M.; Miller, Elliot N.
  • Nature, Vol. 476, Issue 7360, p. 355-359
  • DOI: 10.1038/nature10333

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

  • Dennis, Michael W.; Kolattukudy, P. E.
  • Archives of Biochemistry and Biophysics, Vol. 287, Issue 2, p. 268-275
  • DOI: 10.1016/0003-9861(91)90478-2

Ethanol production from cellulose by coupled saccharification/fermentation usingSaccharomyces cerevisiae and cellulase complex fromSclerotiun rolfsii UV-8 mutant
journal, September 1992

  • Deshpande, Mukund V.
  • Applied Biochemistry and Biotechnology, Vol. 36, Issue 3, p. 227-234
  • DOI: 10.1007/BF02921781

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

  • Dettman, David L.; Reische, Aimee K.; Lohmann, Kyger C.
  • Geochimica et Cosmochimica Acta, Vol. 63, Issue 7-8, p. 1049-1057
  • DOI: 10.1016/S0016-7037(99)00020-4

MUSCLE: a multiple sequence alignment method with reduced time and space complexity
August 2004

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

  • Edgar, R. C.
  • Nucleic Acids Research, Vol. 32, Issue 5, p. 1792-1797
  • DOI: 10.1093/nar/gkh340

Characterizing the metabolic phenotype: A phenotype phase plane analysis
journal, December 2001

  • Edwards, Jeremy S.; Ramakrishna, Ramprasad; Palsson, Bernhard O.
  • Biotechnology and Bioengineering, Vol. 77, Issue 1, p. 27-36
  • DOI: 10.1002/bit.10047

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

[13C]propionate oxidation in wild-type and citrate synthase mutant Escherichia coli: evidence for multiple pathways of propionate utilization
journal, May 1993

  • Evans, C. T.; Sumegi, B.; Srere, P. A.
  • Biochemical Journal, Vol. 291, Issue 3, p. 927-932
  • DOI: 10.1042/bj2910927

A new ferredoxin-dependent carbon reduction cycle in a photosynthetic bacterium.
journal, April 1966

  • Evans, M. C.; Buchanan, B. B.; Arnon, D. I.
  • Proceedings of the National Academy of Sciences, Vol. 55, Issue 4, p. 928-934
  • DOI: 10.1073/pnas.55.4.928

Carbon Isotope Discrimination and Photosynthesis
journal, June 1989

  • Farquhar, G. D.; Ehleringer, J. R.; Hubick, K. T.
  • Annual Review of Plant Physiology and Plant Molecular Biology, Vol. 40, Issue 1, p. 503-537
  • DOI: 10.1146/annurev.pp.40.060189.002443

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

  • Ferenci, T.; Strøm, T.; Quayle, J. R.
  • Biochemical Journal, Vol. 144, Issue 3, p. 477-486
  • DOI: 10.1042/bj1440477

Prokaryotic Genome Size and SSU rDNA Copy Number: Estimation of Microbial Relative Abundance from a Mixed Population
journal, August 1999

  • Fogel, G. B.; Collins, C. R.; Li, J.
  • Microbial Ecology, Vol. 38, Issue 2, p. 93-113
  • DOI: 10.1007/s002489900162

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

  • Fong, Jessica H.; Keating, Amy E.; Singh, Mona
  • Genome Biology, Vol. 5, Issue 2, Article No. R11
  • DOI: 10.1186/gb-2004-5-2-r11

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

  • Friedmann, S.; Alber, B. E.; Fuchs, G.
  • Journal of Bacteriology, Vol. 189, Issue 7, p. 2906-2914
  • DOI: 10.1128/JB.01620-06

Properties of Succinyl-Coenzyme A:L-Malate Coenzyme A Transferase and Its Role in the Autotrophic 3-Hydroxypropionate Cycle of Chloroflexus aurantiacus
journal, March 2006

DNA chips: promising toys have become powerful tools
journal, May 1999

  • Gerhold, David; Rushmore, Thomas; Caskey, C. Thomas
  • Trends in Biochemical Sciences, Vol. 24, Issue 5, p. 168-173
  • DOI: 10.1016/S0968-0004(99)01382-1

Codon catalog usage and the genome hypothesis
journal, January 1980

  • Grantham, R.; Gautier, C.; Gouy, M.
  • Nucleic Acids Research, Vol. 8, Issue 1, p. 197-197
  • DOI: 10.1093/nar/8.1.197-c

Artificially evolved Synechococcus PCC6301 Rubisco variants exhibit improvements in folding and catalytic efficiency
journal, June 2007

  • Greene, Dina N.; Whitney, Spencer M.; Matsumura, Ichiro
  • Biochemical Journal, Vol. 404, Issue 3, p. 517-524
  • DOI: 10.1042/BJ20070071

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

  • Gul-Karaguler, Nevin; Sessions, Richard B.; Clarke, Anthony R.
  • Biotechnology Letters, Vol. 23, Issue 4, p. 283-287
  • DOI: 10.1023/A:1005610414179

Expression of Bacterial Rubisco Genes in Escherichia coli
journal, October 1986

  • Gutteridge, S.; Phillips, A. L.; Kettleborough, C. A.
  • Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 313, Issue 1162, p. 433-445
  • DOI: 10.1098/rstb.1986.0050

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

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

Compilation and analysis of Escherichia coli promoter DNA sequences
journal, January 1983

  • Hawley, Diane K.; McClure, William R.
  • Nucleic Acids Research, Vol. 11, Issue 8, p. 2237-2255
  • DOI: 10.1093/nar/11.8.2237

Fractionation of Carbon and Hydrogen Isotopes in Biosynthetic Processes
journal, January 2001

  • Hayes, J. M.
  • Reviews in Mineralogy and Geochemistry, Vol. 43, Issue 1, p. 225-277
  • DOI: 10.2138/gsrmg.43.1.225

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

  • Henry, Christopher S.; Jankowski, Matthew D.; Broadbelt, Linda J.
  • Biophysical Journal, Vol. 90, Issue 4, p. 1453-1461
  • DOI: 10.1529/biophysj.105.071720

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

  • Henstra, Anne M.; Sipma, Jan; Rinzema, Arjen
  • Current Opinion in Biotechnology, Vol. 18, Issue 3, p. 200-206
  • DOI: 10.1016/j.copbio.2007.03.008

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

  • Herter, Sylvia; Fuchs, Georg; Bacher, Adelbert
  • Journal of Biological Chemistry, Vol. 277, Issue 23, p. 20277-20283
  • DOI: 10.1074/jbc.M201030200

L-Malyl-Coenzyme A Lyase/β-Methylmalyl-Coenzyme A Lyase from Chloroflexus aurantiacus, a Bifunctional Enzyme Involved in Autotrophic CO2 Fixation
journal, November 2002

Mitochondrial trans-2-Enoyl-CoA Reductase of Wax Ester Fermentation from Euglena gracilis Defines a New Family of Enzymes Involved in Lipid Synthesis
journal, November 2004

  • Hoffmeister, Meike; Piotrowski, Markus; Nowitzki, Ulrich
  • Journal of Biological Chemistry, Vol. 280, Issue 6, p. 4329-4338
  • DOI: 10.1074/jbc.M411010200

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

  • Holo, Helge
  • Archives of Microbiology, Vol. 151, Issue 3, p. 252-256
  • DOI: 10.1007/BF00413138

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

  • Hou, J.; Scalcinati, G.; Oldiges, M.
  • Applied and Environmental Microbiology, Vol. 76, Issue 3, p. 851-859
  • DOI: 10.1128/AEM.02040-09

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

Beyond the Calvin Cycle: Autotrophic Carbon Fixation in the Ocean
journal, January 2011

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

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

Towards novel processes for the fine-chemical and pharmaceutical industries
journal, August 2002

Two Tandemly Arranged Ferredoxin Genes in the Hydrogenobacter thermophilus Genome: Comparative Characterization of the Recombinant [4Fe–4S] Ferredoxins
journal, January 2005

  • Ikeda, Takeshi; Yamamoto, Masahiro; Arai, Hiroyuki
  • Bioscience, Biotechnology, and Biochemistry, Vol. 69, Issue 6, p. 1172-1177
  • DOI: 10.1271/bbb.69.1172

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

  • Inokuma, Kentaro; Nakashimada, Yutaka; Akahoshi, Takuya
  • Archives of Microbiology, Vol. 188, Issue 1, p. 37-45
  • DOI: 10.1007/s00203-007-0221-1

C4-dicarboxylate carriers and sensors in bacteria
journal, January 2002

  • Janausch, I. G.; Zientz, E.; Tran, Q. H.
  • Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1553, Issue 1-2, p. 39-56
  • DOI: 10.1016/S0005-2728(01)00233-X

Evolutionary changes in the genetic code
journal, November 1993

  • Jukes, T. H.; Osawa, S.
  • Comparative Biochemistry and Physiology Part B: Comparative Biochemistry, Vol. 106, Issue 3, p. 489-494
  • DOI: 10.1016/0305-0491(93)90122-L

A Novel Bifunctional Wax Ester Synthase/Acyl-CoA:Diacylglycerol Acyltransferase Mediates Wax Ester and Triacylglycerol Biosynthesis in Acinetobacter calcoaceticus ADP1
journal, December 2002

  • Kalscheuer, Rainer; Steinbüchel, Alexander
  • Journal of Biological Chemistry, Vol. 278, Issue 10, p. 8075-8082
  • DOI: 10.1074/jbc.M210533200

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

  • Kalscheuer, Rainer; Stölting, Torsten; Steinbüchel, Alexander
  • Microbiology, Vol. 152, Issue 9, p. 2529-2536
  • DOI: 10.1099/mic.0.29028-0

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

Kinetic and biochemical analyses on the reaction mechanism of a bacterial ATP-citrate lyase
journal, June 2002

Escherichia coli maltose-binding protein is uncommonly effective at promoting the solubility of polypeptides to which it is fused
journal, January 1999

  • Kapust, Rachel B.; Waugh, David S.
  • Protein Science, Vol. 8, Issue 8, p. 1668-1674
  • DOI: 10.1110/ps.8.8.1668

Gene-expression tools for the metabolic engineering of bacteria
journal, November 1999

Measuring the activity of BioBrick promoters using an in vivo reference standard
journal, January 2009

  • Kelly, Jason R.; Rubin, Adam J.; Davis, Joseph H.
  • Journal of Biological Engineering, Vol. 3, Issue 1, Article No. 4
  • DOI: 10.1186/1754-1611-3-4

Autotrophic Metabolism of Formate by Thiobacillus Strain A2
journal, September 1979

  • Kelly, D. P.; Wood, A. P.; Gottschal, J. C.
  • Journal of General Microbiology, Vol. 114, Issue 1, p. 1-13
  • DOI: 10.1099/00221287-114-1-1

Hexose phosphate synthetase from Methylococcus capsulatus makes d–arabino-3-hexulose phosphate
journal, April 1974

  • Kemp, M. B.
  • Biochemical Journal, Vol. 139, Issue 1, p. 129-134
  • DOI: 10.1042/bj1390129

The hexose phosphate synthetase of Methylococcus capsulatus
journal, April 1972

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

  • Kim, O. B.; Unden, G.
  • Journal of Bacteriology, Vol. 189, Issue 5, p. 1597-1603
  • DOI: 10.1128/JB.01402-06

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

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

  • Klimke, William; Agarwala, Richa; Badretdin, Azat
  • Nucleic Acids Research, Vol. 37, Issue suppl_1, p. D216-D223
  • DOI: 10.1093/nar/gkn734

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

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

Rapid monitoring of transesterification and assessing biodiesel fuel quality by near-infrared spectroscopy using a fiber-optic probe
journal, July 1999

Directed evolution of proteins by exon shuffling
journal, May 2001

  • Kolkman, Joost A.; Stemmer, Willem P. C.
  • Nature Biotechnology, Vol. 19, Issue 5, p. 423-428
  • DOI: 10.1038/88084

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

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

  • Larue, T. A.; Kurz, W. G. W.
  • Plant Physiology, Vol. 51, Issue 6, p. 1074-1075
  • DOI: 10.1104/pp.51.6.1074

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

  • Marcia, Marco; Ermler, Ulrich; Peng, Guohong
  • Proteins: Structure, Function, and Bioinformatics, Vol. 78, Issue 5, p. 1073-1083
  • DOI: 10.1002/prot.22665

A New Mechanism for Anaerobic Unsaturated Fatty Acid Formation in Streptococcus pneumoniae
journal, September 2002

  • Marrakchi, Hedia; Choi, Keum-Hwa; Rock, Charles O.
  • Journal of Biological Chemistry, Vol. 277, Issue 47, p. 44809-44816
  • DOI: 10.1074/jbc.M208920200

Mechanistic diversity and regulation of Type II fatty acid synthesis
journal, November 2002

  • Marrakchi, H.; Zhang, Y.-M.; Rock, C. O.
  • Biochemical Society Transactions, Vol. 30, Issue 6, p. 1050-1055
  • DOI: 10.1042/bst0301050

Rehosting of Bacterial Chaperones for High-Quality Protein Production
journal, October 2009

  • Martinez-Alonso, M.; Toledo-Rubio, V.; Noad, R.
  • Applied and Environmental Microbiology, Vol. 75, Issue 24, p. 7850-7854
  • DOI: 10.1128/AEM.01532-09

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

  • Martínez-Alonso, Mónica; García-Fruitós, Elena; Ferrer-Miralles, Neus
  • Microbial Cell Factories, Vol. 9, Issue 1, Article No. 64
  • DOI: 10.1186/1475-2859-9-64

Protein evolution by molecular breeding
journal, June 1999

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

  • Stackebrandt, E.; Jeanthon, C.; Kostrikina, N. A.
  • International Journal of Systematic and Evolutionary Microbiology, Vol. 52, Issue 4, p. 1299-1304
  • DOI: 10.1099/00207713-52-4-1299

High-precision continuous-flow isotope ratio mass spectrometry
journal, January 1997

KAAS: an automatic genome annotation and pathway reconstruction server
journal, May 2007

  • Moriya, Y.; Itoh, M.; Okuda, S.
  • Nucleic Acids Research, Vol. 35, Issue S2, p. W182-W185
  • DOI: 10.1093/nar/gkm321

Developments and perspectives of photobioreactors for biofuel production
journal, June 2010

  • Morweiser, Michael; Kruse, Olaf; Hankamer, Ben
  • Applied Microbiology and Biotechnology, Vol. 87, Issue 4, p. 1291-1301
  • DOI: 10.1007/s00253-010-2697-x

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

  • Orita, Izumi; Sakamoto, Naoki; Kato, Nobuo
  • Applied Microbiology and Biotechnology, Vol. 76, Issue 2, p. 439-445
  • DOI: 10.1007/s00253-007-1023-8

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

The Ribulose Monophosphate Pathway Substitutes for the Missing Pentose Phosphate Pathway in the Archaeon Thermococcus kodakaraensis
journal, June 2006

  • Orita, I.; Sato, T.; Yurimoto, H.
  • Journal of Bacteriology, Vol. 188, Issue 13, p. 4698-4704
  • DOI: 10.1128/JB.00492-06

Enhancement and Selective Production of Phoslactomycin B, a Protein Phosphatase IIa Inhibitor, through Identification and Engineering of the Corresponding Biosynthetic Gene Cluster
journal, June 2003

  • Palaniappan, Nadaraj; Kim, Beom Seok; Sekiyama, Yasuyo
  • Journal of Biological Chemistry, Vol. 278, Issue 37, p. 35552-35557
  • DOI: 10.1074/jbc.M305082200

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

  • Parikh, Monal R.; Greene, Dina N.; Woods, Kristen K.
  • Protein Engineering, Design and Selection, Vol. 19, Issue 3, p. 113-119
  • DOI: 10.1093/protein/gzj010

New Pathway for Long-Chain n-Alkane Synthesis via 1-Alcohol in Vibrio furnissii M1
journal, February 2005

A Novel Δ32-Enoyl-CoA Isomerase Involved in the Biosynthesis of the Cyclohexanecarboxylic Acid-Derived Moiety of the Polyketide Ansatrienin A
journal, June 2000

  • Patton, Stephanie M.; Cropp, T. Ashton; Reynolds, Kevin A.
  • Biochemistry, Vol. 39, Issue 25, p. 7595-7604
  • DOI: 10.1021/bi0005714

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

Discoveries in Rubisco (Ribulose 1,5-bisphosphate carboxylase/oxygenase): a historical perspective
journal, July 2007

  • Portis, Archie R.; Parry, Martin A. J.
  • Photosynthesis Research, Vol. 94, Issue 1, p. 121-143
  • DOI: 10.1007/s11120-007-9225-6

Effect of Escherichia coli biomass composition on central metabolic fluxes predicted by a stoichiometric model
journal, October 1998

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

  • Rathnasingh, Chelladurai; Raj, Subramanian Mohan; Lee, Youjin
  • Journal of Biotechnology, Vol. 157, Issue 4, p. 633-640
  • DOI: 10.1016/j.jbiotec.2011.06.008

Quorum sensing: the many languages of bacteria
journal, January 2006

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

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

  • Roessner, C. A.; Spencer, J. B.; Ozaki, S.
  • Protein Expression and Purification, Vol. 6, Issue 2, p. 155-163
  • DOI: 10.1006/prep.1995.1019

[20] Fusions to maltose-binding protein: Control of folding and solubility in protein purification
book, January 2000

  • Sachdev, Deepali; Chirgwin, John M.
  • Applications of Chimeric Genes and Hybrid Proteins Part A: Gene Expression and Protein Purification, p. 312-321
  • DOI: 10.1016/S0076-6879(00)26062-X

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

  • Sachdev, Deepali; Chirgwin, John M.
  • Protein Expression and Purification, Vol. 12, Issue 1, p. 122-132
  • DOI: 10.1006/prep.1997.0826

The neighbor-joining method: a new method for reconstructing phylogenetic trees.
journal, July 1987

Carbon isotopic fractionation associated with lipid biosynthesis by a cyanobacterium: Relevance for interpretation of biomarker records
journal, December 1997

  • Sakata, Susumu; Hayes, John M.; McTaggart, Andrew R.
  • Geochimica et Cosmochimica Acta, Vol. 61, Issue 24, p. 5379-5389
  • DOI: 10.1016/S0016-7037(97)00314-1

Metabolic Engineering through Cofactor Manipulation and Its Effects on Metabolic Flux Redistribution in Escherichia coli
journal, April 2002

  • San, Ka-Yiu; Bennett, George N.; Berrı́os-Rivera, Susana J.
  • Metabolic Engineering, Vol. 4, Issue 2, p. 182-192
  • DOI: 10.1006/mben.2001.0220

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

  • Sauer, Uwe; Canonaco, Fabrizio; Heri, Sylvia
  • Journal of Biological Chemistry, Vol. 279, Issue 8, p. 6613-6619
  • DOI: 10.1074/jbc.M311657200

Methanol-based industrial biotechnology: current status and future perspectives of methylotrophic bacteria
journal, February 2009

Sulfide-Quinone Reductase from Rhodobacter capsulatus: Purification, Cloning, And Expression
journal, April 1997

  • Schütz, Michael; Shahak, Yosepha; Padan, Etana
  • Journal of Biological Chemistry, Vol. 272, Issue 15, p. 9890-9894
  • DOI: 10.1074/jbc.272.15.9890

Expression and Regulation of a Silent Operon, hyf, Coding for Hydrogenase 4 Isoenzyme in Escherichia coli
journal, December 2003

Engineering of coenzyme specificity of formate dehydrogenase from Saccharomyces cerevisiae
journal, November 2002

  • Serov, Alexander E.; Popova, Anna S.; Fedorchuk, Vladimir V.
  • Biochemical Journal, Vol. 367, Issue 3, p. 841-847
  • DOI: 10.1042/bj20020379

Chapter thirteen - Assembly of BioBrick Standard Biological Parts Using Three Antibiotic Assembly
book, January 2011

  • Shetty, Reshma; Lizarazo, Meagan; Rettberg, Randy
  • Synthetic Biology, Part B - Computer Aided Design and DNA Assembly, p. 311-326
  • DOI: 10.1016/B978-0-12-385120-8.00013-9

Engineering BioBrick vectors from BioBrick parts
journal, January 2008

  • Shetty, Reshma P.; Endy, Drew; Knight, Thomas F.
  • Journal of Biological Engineering, Vol. 2, Article No. 5
  • DOI: 10.1186/1754-1611-2-5

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

  • Shibata, Hiroomi; Kobayashi, Shigeki
  • Canadian Journal of Microbiology, Vol. 47, Issue 9, p. 855-860
  • DOI: 10.1139/w01-090

book, January 1997

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

  • Smith, J. L.; Campbell, B. J.; Hanson, T. E.
  • International Journal of Systematic and Evolutionary Microbiology, Vol. 58, Issue 7, p. 1598-1602
  • DOI: 10.1099/ijs.0.65435-0

Effect of copy number and mRNA processing and stabilization on transcript and protein levels from an engineered dual-gene operon
journal, April 2002

  • Smolke, Christina D.; Keasling, Jay D.
  • Biotechnology and Bioengineering, Vol. 78, Issue 4, p. 412-424
  • DOI: 10.1002/bit.10218

Effect of gene location, mRNA secondary structures, and RNase sites on expression of two genes in an engineered operon
journal, October 2002

  • Smolke, Christina D.; Keasling, Jay D.
  • Biotechnology and Bioengineering, Vol. 80, Issue 7, p. 762-776
  • DOI: 10.1002/bit.10434

Controlling the Metabolic Flux through the Carotenoid Pathway Using Directed mRNA Processing and Stabilization
journal, October 2001

  • Smolke, Christina D.; Martin, Vincent J. J.; Keasling, Jay D.
  • Metabolic Engineering, Vol. 3, Issue 4, p. 313-321
  • DOI: 10.1006/mben.2001.0194

Coordinated, Differential Expression of Two Genes through Directed mRNA Cleavage and Stabilization by Secondary Structures
journal, December 2000

Enzymes of a novel autotrophic CO2 fixation pathway in the phototrophic bacterium Chloroflexus aurantiacus, the 3-hydroxypropionate cycle
journal, August 1993

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

  • Strøm, T.; Ferenci, T.; Quayle, J. R.
  • Biochemical Journal, Vol. 144, Issue 3, p. 465-476
  • DOI: 10.1042/bj1440465

Heterologous Expression and Maturation of an NADP-Dependent [NiFe]-Hydrogenase: A Key Enzyme in Biofuel Production
journal, May 2010

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

  • Tabita, F. R.; Small, C. L.
  • Proceedings of the National Academy of Sciences, Vol. 82, Issue 18, p. 6100-6103
  • DOI: 10.1073/pnas.82.18.6100

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

  • Tatusov, Roman L.; Fedorova, Natalie D.; Jackson, John D.
  • BMC Bioinformatics, Vol. 4, Article No. 41
  • DOI: 10.1186/1471-2105-4-41

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

Regulation of quorum sensing in Pseudomonas
journal, March 2006

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

  • Vignais, Paulette M.; Billoud, Bernard
  • Chemical Reviews, Vol. 107, Issue 10, p. 4206-4272
  • DOI: 10.1021/cr050196r

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

Carboxylation reaction catalyzed by 2-oxoglutarate:ferredoxin oxidoreductases from Hydrogenobacter thermophilus
journal, November 2009

  • Yamamoto, Masahiro; Ikeda, Takeshi; Arai, Hiroyuki
  • Extremophiles, Vol. 14, Issue 1, p. 79-85
  • DOI: 10.1007/s00792-009-0289-4

Purification and characterization of pyruvate:ferredoxin oxidoreductase from Hydrogenobacter thermophilus TK-6
journal, April 1997

  • Yoon, Ki-Seok; Ishii, Masaharu; Kodama, Tohru
  • Archives of Microbiology, Vol. 167, Issue 5, p. 275-279
  • DOI: 10.1007/s002030050443

Coassimilation of Organic Substrates via the Autotrophic 3-Hydroxypropionate Bi-Cycle in Chloroflexus aurantiacus
journal, July 2011

  • Zarzycki, Jan; Fuchs, Georg
  • Applied and Environmental Microbiology, Vol. 77, Issue 17, p. 6181-6188
  • DOI: 10.1128/AEM.00705-11

Identifying the missing steps of the autotrophic 3-hydroxypropionate CO2 fixation cycle in Chloroflexus aurantiacus
journal, December 2009

  • Zarzycki, Jan; Brecht, Volker; Müller, Michael
  • Proceedings of the National Academy of Sciences, Vol. 106, Issue 50, p. 21317-21322
  • DOI: 10.1073/pnas.0908356106

InterProScan - an integration platform for the signature-recognition methods in InterPro
journal, September 2001

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

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

  • Zhang, Yong-Mei; Marrakchi, Hedia; Rock, Charles O.
  • Journal of Biological Chemistry, Vol. 277, Issue 18, p. 15558-15565
  • DOI: 10.1074/jbc.M201399200

Production of ubiquinone in Escherichia coli by expression of various genes responsible for ubiquinone biosynthesis
journal, January 1995

  • Zhu, Xufen; Yuasa, Mihoko; Okada, Kazunori
  • Journal of Fermentation and Bioengineering, Vol. 79, Issue 5, p. 493-495
  • DOI: 10.1016/0922-338X(95)91268-A

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