Stoichiometric and energetic analyses of non-photosynthetic CO2-fixation pathways to support synthetic biology strategies for production of fuels and chemicals

National Academy of Sciences (U.S.), 2009

Hawkins, 2011, Extremely thermophilic routes to microbial electrofuels, ACS Catal, 1, 1043, 10.1021/cs2003017

Li, 2012, Integrated electromicrobial conversion of CO2 to higher alcohols, Science, 335, 1596, 10.1126/science.1217643

Papoutsakis, 1984, Equations and calculations for fermentations of butyric-acid bacteria, Biotechnol Bioeng, 26, 174, 10.1002/bit.260260210

Papoutsakis, 1985, Equations and calculations of product yields and preferred pathways for butanediol and mixed-acid fermentations, Biotechnol Bioeng, 27, 50, 10.1002/bit.260270108

Papoutsakis, 1985, Fermentation equations for propionic-acid bacteria and production of assorted oxychemicals from various sugars, Biotechnol Bioeng, 27, 67, 10.1002/bit.260270109

Edwards, 1999, Ch. 2 Metabolic flux balance analysis, 13

Papoutsakis, 2008, Engineering solventogenic clostridia, Curr Opin Biotechnol, 19, 420, 10.1016/j.copbio.2008.08.003

Tracy, 2012, Clostridia: the importance of their exceptional substrate and metabolite diversity for biofuel and biorefinery applications, Curr Opin Biotechnol, 23, 364, 10.1016/j.copbio.2011.10.008

Lutke-Eversloh, 2011, Metabolic engineering of Clostridium acetobutylicum: recent advances to improve butanol production, Curr Opin Biotechnol, 22, 634, 10.1016/j.copbio.2011.01.011

Calvin, 1948, The path of carbon in photosynthesis, Science, 107, 476, 10.1126/science.107.2784.476

Pohlmann, 2006, Genome sequence of the bioplastic-producing “Knallgas” bacterium Ralstonia eutropha H16, Nat Biotechnol, 24, 1257, 10.1038/nbt1244

Evans, 1966, A new ferredoxin-dependent carbon reduction cycle in a photosynthetic bacterium, Proc Natl Acad Sci USA, 55, 928, 10.1073/pnas.55.4.928

Campbell, 2006, The versatile epsilon-proteobacteria: key players in sulphidic habitats, Nat Rev Microbiol, 4, 458, 10.1038/nrmicro1414

Arai, 2010, Complete genome sequence of the thermophilic, obligately chemolithoautotrophic hydrogen-oxidizing bacterium Hydrogenobacter thermophilus TK-6, J Bacteriol, 192, 2651, 10.1128/JB.00158-10

Wood, 1991, Life with CO or CO2 and H2 as a source of carbon and energy, FASEB J, 5, 156, 10.1096/fasebj.5.2.1900793

Herter, 2002, A bicyclic autotrophic CO2 fixation pathway in Chloroflexus aurantiacus, J Biol Chem, 277, 20277, 10.1074/jbc.M201030200

Berg, 2007, A 3-hydroxypropionate/4-hydroxybutyrate autotrophic carbon dioxide assimilation pathway in Archaea, Science, 318, 1782, 10.1126/science.1149976

Huber, 2008, A dicarboxylate/4-hydroxybutyrate autotrophic carbon assimilation cycle in the hyperthermophilic Archaeum Ignicoccus hospitalis, Proc Natl Acad Sci USA, 105, 7851, 10.1073/pnas.0801043105

Alber, 2006, Malonyl-coenzyme A reductase in the modified 3-hydroxypropionate cycle for autotrophic carbon fixation in archaeal Metallosphaera and Sulfolobus spp, J Bacteriol, 188, 8551, 10.1128/JB.00987-06

Boyle, 2011, Computation of metabolic fluxes and efficiencies for biological carbon dioxide fixation, Metab Eng, 13, 150, 10.1016/j.ymben.2011.01.005

Bar-Even, 2010, Design and analysis of synthetic carbon fixation pathways, Proc Natl Acad Sci USA, 107, 8889, 10.1073/pnas.0907176107

Berg, 2010, Autotrophic carbon fixation in Archaea, Nat Rev Microbiol, 8, 447, 10.1038/nrmicro2365

Schiel-Bengelsdorf, 2012, Pathway engineering and synthetic biology using acetogens, FEBS Lett, 586, 2191, 10.1016/j.febslet.2012.04.043

Köpke, 2011, Fermentative production of ethanol from carbon monoxide, Curr Opin Biotechnol, 22, 320, 10.1016/j.copbio.2011.01.005

Nevin, 2011, Electrosynthesis of organic compounds from carbon dioxide is catalyzed by a diversity of acetogenic microorganisms, Appl Environ Microbiol, 77, 2882, 10.1128/AEM.02642-10

Köpke, 2010, Clostridium ljungdahlii represents a microbial production platform based on syngas, Proc Natl Acad Sci USA, 107, 13087, 10.1073/pnas.1004716107

Bi, 2011, SpoIIE is necessary for asymmetric division, sporulation, and expression of sigma(F), sigma(E), and sigma(G) but does not control solvent production in Clostridium acetobutylicum ATCC 824, J Bacteriol, 193, 5130, 10.1128/JB.05474-11

Jones, 2011, Inactivation of sigma(F) in Clostridium acetobutylicum ATCC 824 blocks sporulation prior to asymmetric division and abolishes sigma(E) and sigma(G) protein expression but does not block solvent formation, J Bacteriol, 193, 2429, 10.1128/JB.00088-11

Tracy, 2011, Inactivation of sigma(E) and sigma(G) in Clostridium acetobutylicum illuminates their roles in clostridial-cell-form biogenesis, granulose synthesis, solventogenesis, and spore morphogenesis, J Bacteriol, 193, 1414, 10.1128/JB.01380-10

Heap, 2007, The ClosTron: a universal gene knock-out system for the genus Clostridium, J Microbiol Methods, 70, 452, 10.1016/j.mimet.2007.05.021

Al-Hinai MA, Fast AG, Papoutsakis ET: A novel system for efficient isolation of double-crossover allelic exchange mutants in Clostridium enabling markerless chromosomal gene deletions and DNA integration. Appl Environ Microbiol, http://dx.doi.org/10.1128/AEM.02214-12, in press.

Park, 2010, Development of a gene knockout system for Ralstonia eutropha H16 based on the broad-host-range vector expressing a mobile group II intron, FEMS Microbiol Lett, 309, 193

Leigh, 2011, Model organisms for genetics in the domain Archaea: methanogens, halophiles, Thermococcales and Sulfolobales, FEMS Microbiol Rev, 35, 577, 10.1111/j.1574-6976.2011.00265.x

Payne, 1970, Energy yields and growth of heterotrophs, Annu Rev Microbiol, 24, 17, 10.1146/annurev.mi.24.100170.000313

Thauer, 2008, Methanogenic archaea: ecologically relevant differences in energy conservation, Nat Rev Microbiol, 6, 579, 10.1038/nrmicro1931

Fuchs, 1986, CO2 fixation in acetogenic bacteria – variations on a theme, FEMS Microbiol Rev, 39, 181, 10.1111/j.1574-6968.1986.tb01859.x

Moodie, 1990, Microbial anaerobic respiration, 225

Daniel, 1990, Characterization of the H2- and CO-dependent chemolithotrophic potentials of the acetogens Clostridium thermoaceticum and Acetogenium kivui, J Bacteriol, 172, 4464, 10.1128/jb.172.8.4464-4471.1990

Annous, 1996, Regulation of hydrogen metabolism in Butyribacterium methylotrophicum by substrate and pH, Appl Microbiol Biotechnol, 45, 804, 10.1007/s002530050766

Hugler, 2007, Autotrophic CO2 fixation via the reductive tricarboxylic acid cycle in different lineages within the phylum Aquificae: evidence for two ways of citrate cleavage, Environ Microbiol, 9, 81, 10.1111/j.1462-2920.2006.01118.x

Auernik, 2008, Identification of components of electron transport chains in the extremely thermoacidophilic crenarchaeon Metallosphaera sedula through iron and sulfur compound oxidation transcriptomes, Appl Environ Microbiol, 74, 7723, 10.1128/AEM.01545-08

Müller, 2003, Energy conservation in acetogenic bacteria, Appl Environ Microbiol, 69, 6345, 10.1128/AEM.69.11.6345-6353.2003

Pierce, 2008, The complete genome sequence of Moorella thermoacetica (f. Clostridium thermoaceticum), Environ Microbiol, 10, 2550, 10.1111/j.1462-2920.2008.01679.x

Müller, 2008, Discovery of a ferredoxin:NAD+-oxidoreductase (Rnf) in Acetobacterium woodii: a novel potential coupling site in acetogens, Ann N Y Acad Sci, 1125, 137, 10.1196/annals.1419.011

Simon, 1987, Reduction of 2-enoates and alkanoates with carbon-monoxide or formate, viologens, and clostridium thermoaceticum to saturated acids and unsaturated and saturated alcohols, Angew Chem Int Ed Engl, 26, 785, 10.1002/anie.198707851

White, 1992, The role of tungstate and or molybdate in the formation of aldehyde oxidoreductase in Clostridium thermoaceticum and other acetogens – immunological distances of such enzymes, Arch Microbiol, 158, 81, 10.1007/BF00245209

Huber, 1994, Further characterization of two different, reversible aldehyde oxidoreductases from Clostridium formicoaceticum, one containing tungsten and the other molybdenum, Arch Microbiol, 162, 303, 10.1007/BF00263776

Peters, 1998, Efficiency of hydrogen utilization during unitrophic and mixotrophic growth of Acetobacterium woodii on hydrogen and lactate in the chemostat, FEMS Microbiol Ecol, 26, 317, 10.1111/j.1574-6941.1998.tb00516.x

Braun, 1981, Effect of molecular-hydrogen and carbon-dioxide on chemo-organotrophic growth of Acetobacterium woodii and Clostridium aceticum, Arch Microbiol, 128, 294, 10.1007/BF00422533

Bruant, 2010, Genomic analysis of carbon monoxide utilization and butanol production by Clostridium carboxidivorans strain P7T, PLoS ONE, 5, e13033, 10.1371/journal.pone.0013033

Grethlein, 1991, Evidence for production of n-butanol from carbon monoxide by Butyribacterium methylotrophicum, J Ferment Bioeng, 72, 58, 10.1016/0922-338X(91)90147-9

Köpke, 2011, 2,3-butanediol production by acetogenic bacteria, an alternative route to chemical synthesis, using industrial waste gas, Appl Environ Microbiol, 77, 5467, 10.1128/AEM.00355-11

Ji, 2011, Microbial 2,3-butanediol production: a state-of-the-art review, Biotechnol Adv, 29, 351, 10.1016/j.biotechadv.2011.01.007

Stephanopoulos G: Patent application: converting a carbon source into a lipid comprises culturing a first organism in the presence of a carbon source and culturing a second organism in the presence of carbon dioxide. Massachusetts Inst Technology (MA); 2011:27 pp. US2011177564-A2011177561 US2011007325 2011177514 Jan 2011172011 WO2011088364-A2011177562 WOUS2011021360 2011177514 Jan 2011172011 WO2011088364-A2011177568 WOUS2011021360 2011177514 Jan 2011172011 WO2011088364-A2011177563 WOUS2011021360 2011177514 Jan 2011172011.

Kusian, 1997, Organization and regulation of cbb CO2 assimilation genes in autotrophic bacteria, FEMS Microbiol Rev, 21, 135, 10.1111/j.1574-6976.1997.tb00348.x

Fischbach, 2010, Prokaryotic gene clusters: a rich toolbox for synthetic biology, Biotechnol J, 5, 1277, 10.1002/biot.201000181

Lutke-Eversloh, 2008, Combinatorial pathway analysis for improved L-tyrosine production in Escherichia coli: identification of enzymatic bottlenecks by systematic gene overexpression, Metab Eng, 10, 69, 10.1016/j.ymben.2007.12.001

Lee, 2007, Systems metabolic engineering of Escherichia coli for L-threonine production, Mol Syst Biol, 3, 149, 10.1038/msb4100196

Farmer, 2000, Improving lycopene production in Escherichia coli by engineering metabolic control, Nat Biotechnol, 18, 533, 10.1038/75398

Leonard, 2010, Combining metabolic and protein engineering of a terpenoid biosynthetic pathway for overproduction and selectivity control, Proc Natl Acad Sci USA, 107, 13654, 10.1073/pnas.1006138107

Boyle, 2012, Tools for genome-wide strain design and construction, Curr Opin Biotechnol, 10.1016/j.copbio.2012.01.012

Jensen, 1998, The sequence of spacers between the consensus sequences modulates the strength of prokaryotic promoters, Appl Environ Microbiol, 64, 82, 10.1128/AEM.64.1.82-87.1998

Pfleger, 2006, Combinatorial engineering of intergenic regions in operons tunes expression of multiple genes, Nat Biotechnol, 24, 1027, 10.1038/nbt1226

Salis, 2009, Automated design of synthetic ribosome binding sites to control protein expression, Nat Biotechnol, 27, 946, 10.1038/nbt.1568

Gibson, 2009, Enzymatic assembly of DNA molecules up to several hundred kilobases, Nat Methods, 6, 343, 10.1038/nmeth.1318

Wang, 2009, Programming cells by multiplex genome engineering and accelerated evolution, Nature, 460, 10.1038/nature08187

Warner, 2010, Rapid profiling of a microbial genome using mixtures of barcoded oligonucleotides, Nat Biotechnol, 28, 10.1038/nbt.1653

de Marco, 2007, Protocol for preparing proteins with improved solubility by co-expressing with molecular chaperones in Escherichia coli, Nat Protoc, 2, 2632, 10.1038/nprot.2007.400

de Marco, 2007, Chaperone-based procedure to increase yields of soluble recombinant proteins produced in E. coli, BMC Biotechnol, 7, 32, 10.1186/1472-6750-7-32

Nicolaou, 2010, A comparative view of metabolite and substrate stress and tolerance in microbial bioprocessing: from biofuels and chemicals, to biocatalysis and bioremediation, Metab Eng, 12, 307, 10.1016/j.ymben.2010.03.004

Kozak, 2005, Regulation of translation via mRNA structure in prokaryotes and eukaryotes, Gene, 361, 13, 10.1016/j.gene.2005.06.037

Gottesman, 2004, The small RNA regulators of Escherichia coli: roles and mechanisms, Annu Rev Microbiol, 58, 303, 10.1146/annurev.micro.58.030603.123841

Serganov, 2007, Ribozymes, riboswitches and beyond: regulation of gene expression without proteins, Nat Rev Genet, 8, 776, 10.1038/nrg2172

Nicolaou, 2011, Coexisting/Coexpressing Genomic Libraries (CoGeL) identify interactions among distantly located genetic loci for developing complex microbial phenotypes, Nucleic Acids Res, 39, 152, 10.1093/nar/gkr817

Borden, 2010, A genomic-library based discovery of a novel, possibly synthetic, acid-tolerance mechanism in Clostridium acetobutylicum involving non-coding RNAs and ribosomal RNA processing, Metab Eng, 12, 268, 10.1016/j.ymben.2009.12.004

Borden, 2007, Dynamics of genomic-library enrichment and identification of solvent tolerance genes for Clostridium acetobutylicum, Appl Environ Microbiol, 73, 3061, 10.1128/AEM.02296-06