Metabolic engineering in chemolithoautotrophic hosts for the production of fuels and chemicals

Metabolic Engineering

Volumn 30, Issue , 2015, Pages 105-120

  Nybo, S Eric ^a   Khan, Nymul E ^b   Woolston, Benjamin M ^c   Curtis, Wayne R ^b  

^a FERRIS STATE UNIVERSITY   (United States)

^b The Pennsylvania State University   (United States)

^c Massachusetts Institute of Technology Cambridge   (United States)

Author keywords

Acetogen; Biochemicals; Biofuels; CO2< inf> fixation; Electrosynthesis; Genetic transformation; Hydrogenase

Indexed keywords

AMINO ACIDS; BACTERIA; BIOFUELS; BIOLOGY; CARBON; CHEMICAL COMPOUNDS; GREENHOUSE GASES; METABOLISM; NUCLEIC ACIDS; PRODUCTION PLATFORMS; SUBSTRATES;

ACETOGEN; BIOCHEMICALS; ELECTROSYNTHESIS; GENETIC TRANSFORMATION; HYDROGENASES;

METABOLIC ENGINEERING;

CARBON; FUEL; HYDROGEN; BIOFUEL;

BIOREACTOR DESIGN; CARBON FIXATION; CHEMOLITHOAUTOTROPH; CHEMOLITHOTROPH; GENETIC MANIPULATION; GENETIC TRANSFORMATION; HOST; METABOLIC ENGINEERING; NONHUMAN; PLASMID; PRIORITY JOURNAL; RALSTONIA; REVIEW; RHODOBACTER; SCALE UP; GENETICS; METABOLISM; PROCEDURES;

BACTERIA (MICROORGANISMS); PROKARYOTA; PROTEOBACTERIA; RALSTONIA; RHODOBACTER;

BIOFUELS; METABOLIC ENGINEERING; RALSTONIA; RHODOBACTER;

EID: 84930945149     PISSN: 10967176     EISSN: 10967184     Source Type: Journal    
DOI: 10.1016/j.ymben.2015.04.008     Document Type: Review

References (129)

1. Al-Hinai M.A., Fast A.G., Papoutsakis E.T. Novel system for efficient isolation of clostridium double-crossover allelic exchange mutants enabling markerless chromosomal gene deletions and DNA integration. Appl. Environ. Microbiol. 2012, 78(22):8112-8121.
2. Badger M.R., Bek E.J. Multiple Rubisco forms in proteobacteria: their functional significance in relation to CO2 acquisition by the CBB cycle. J. Exp. Bot. 2008, 59(7):1525-1541. Available at: http://www.ncbi.nlm.nih.gov/pubmed/18245799
3. Banerjee, A., Leang, C., Ueki, T., Nevin, K.P., Lovley, D.R., 2014. A lactose-inducible system for metabolic engineering of Clostridium ljungdahlii.
4. Banta, S., West, A., 2014. Electrofuel production using genetically engineered Acidithiobacillus ferrooxidans. In: Electrochemical Society Meeting Abstracts. The Society for Solid-state and Electrochemical Science and Technology. Available at: http://ma.ecsdl.org/content/MA2014-02/50/2290.abstract.
5. Bar-Even A., Noor E., Milo R. A survey of carbon fixation pathways through a quantitative lens. J. Exp. Bot. 2012, 63(6):2325-2342. Available at: http://www.ncbi.nlm.nih.gov/pubmed/22200662
6. Barnard G.C., Henderson G.E., Srinivasan S., Gerngross T.U. High level recombinant protein expression in Ralstonia eutropha using T7 RNA polymerase based amplification. Protein Expr. Purif. 2004, 38(2):264-271. Available at: http://www.ncbi.nlm.nih.gov/pubmed/15555942
7. Bayrock D.P., Ingledew W.M. Ethanol production in multistage continuous, single stage continuous, Lactobacillus-contaminated continuous, and batch fermentations. World J. Microbiol. Biotechnol. 2005, 21(1980):83-88.
8. Beekwilder J., van Houwelingen A., Cankar K., van Dijk A.D.J., de Jong R.M., et al. Valencene synthase from the heartwood of Nootka cypress (Callitropsis nootkatensis) for biotechnological production of valencene. Plant Biotechnol. J. 2014, 12:174-182. Available at: http://www.ncbi.nlm.nih.gov/pubmed/24112147
9. Bengelsdorf F.R., Straub M., Dürre P. Bacterial synthesis gas (syngas) fermentation. Environ. Technol. 2013, 34(13-16):1639-1651. Available at: http://www.ncbi.nlm.nih.gov/pubmed/24350425
10. Berg I. Ecological aspects of the distribution of different autotrophic CO2 fixation pathways. Appl. Environ. Microbiol. 2011, 77(6):1925-1936. Available at: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3067309&tool=pmcentrez&rendertype=abstract
11. Berg, J.M., Tymoczko, J.L., Stryer, L., 2002. Biochemistry 5th ed., W.H. Freeman, New York, NY. Available at: http://www.ncbi.nlm.nih.gov/books/NBK22519/.
12. Berzin V., Kiriukhin M., Tyurin M. Selective production of acetone during continuous synthesis gas fermentation by engineered biocatalyst Clostridium sp. MAceT113. Lett. Appl. Microbiol. 2012, 55(2):149-154. Available at: http://www.ncbi.nlm.nih.gov/pubmed/22642684
13. Berzin V., Tyurin M., Kiriukhin M. Selective n-butanol production by Clostridium sp. MTButOH1365 during continuous synthesis gas fermentation due to expression of synthetic thiolase, 3-hydroxy butyryl-CoA dehydrogenase, crotonase, butyryl-CoA dehydrogenase, butyraldehyde dehydrogenase, and. Appl. Biochem. Biotechnol. 2013, 169(3):950-959. Available at: http://www.ncbi.nlm.nih.gov/pubmed/23292245
14. Bi C., Su P., Müller J., Yeh Y.-C., Chhabra S.R., et al. Development of a broad-host synthetic biology toolbox for Ralstonia eutropha and its application to engineering hydrocarbon biofuel production. Microb. Cell Fact. 2013, 12:107. Available at: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3831590&tool=pmcentrez&rendertype=abstract
15. Böck A., King P.W., Blokesch M., Posewitz M.C. Maturation of hydrogenases. Adv. Microb. Physiol. 2006, 51:1-71. Available at: http://www.ncbi.nlm.nih.gov/pubmed/17091562
16. Bongers L. Energy generation and utilization in hydrogen bacteria. J. Bacteriol. 1970, 104(1):145-151. Available at: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=248194&tool=pmcentrez&rendertype=abstract
17. Braakman R., Smith E. Metabolic evolution of a deep-branching hyperthermophilic chemoautotrophic bacterium. PLoS One 2014, 9.
18. Cantet J., Bergel A., Comtat M. Kinetics of the catalysis by the Alcaligenes eutrophus H16 kinetics of the catalysis by the Alcaligenes eutrophus H16 hydrogenase of the electrochemical reduction of NAD+. J. Mol. Catal. 1992, 73(3):371-380. Available at: http://www.sciencedirect.com/science/journal/03045102/73
19. Cheng S., Xing D., Call D.F., Logan B.E. Direct biological conversion of electrical current into methane by electromethanogenesis. Environ. Sci. Technol. 2009, 43(10):3953-3958.
20. Cho C., Jang Y., Moon H.G., Lee J., Lee S.Y. Metabolic engineering of clostridia for the production of chemicals. Biofuels Bioprod. Biorefin. 2014, Available at: http://doi.wiley.com/10.1002/bbb.1531
21. Choi J.Il., Lee S.Y., Han K. Cloning of the Alcaligenes latus polyhydroxyalkanoate biosynthesis genes and use of these genes for enhanced production of poly(3-hydroxybutyrate) in Escherichia coli. Appl. Environ. Microbiol. 1998, 64(12):4897-4903.
22. Daniell, J., Köpke, M., Simpson, S., 2012. Commercial Biomass Syngas Fermentation. Available at: http://www.mdpi.com/1996-1073/5/12/5372/.
23. Datsenko K.A., Wanner B.L. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl. Acad. Sci. USA 2000, 97:6640-6645.
24. Delamarre S.C., Batt C. Comparative study of promoters for the production of polyhydroxyalkanoates in recombinant strains of Wautersia eutropha. Appl. Microbiol. Biotechnol. 2006, 71(5):668-679. Available at: http://www.ncbi.nlm.nih.gov/pubmed/16362422
25. Demirel B., Scherer P. The roles of acetotrophic and hydrogenotrophic methanogens during anaerobic conversion of biomass to methane: a review. Rev. Environ. Sci. Bio/Technol. 2008, 7(2):173-190. Available at: http://link.springer.com/10.1007/s11157-008-9131-1
26. Ditta G., Schmidhauser T., Yakobson E., Lu P., Liang X.W., et al. Plasmids related to the broad host range vector, pRK290, useful for gene cloning and for monitoring gene expression. Plasmid 1985, 13(2):149-153. Available at: http://www.ncbi.nlm.nih.gov/pubmed/2987994
27. Drake H.L., Daniel S.L. Physiology of the thermophilic acetogen Moorella thermoacetica. Res. Microbiol. 2004, 155(10):869-883.
28. Dumsday G.J., Zhou B., Yaqin W., Stanley G.a, Pamment N.B. Comparative stability of ethanol production by Escherichia coli KO11 in batch and chemostat culture. J. Ind. Microbiol. Biotechnol. 1999, 23:701-708. Available at: http://link.springer.com/10.1038/sj.jim.2900690
29. Fang L., Lin H.X., Low C.S., Wu M.H., Chow Y., et al. Expression of the Chlamydomonas reinhardtii sedoheptulose-1,7-bisphosphatase in Dunaliella bardawil leads to enhanced photosynthesis and increased glycerol production. Plant Biotechnol. J. 2012, 10(9):1129-1135. Available at: http://www.ncbi.nlm.nih.gov/pubmed/22998361
30. Fast A.G., Papoutsakis E.T. Stoichiometric and energetic analyses of non-photosynthetic CO2-fixation pathways to support synthetic biology strategies for production of fuels and chemicals. Curr. Opin. Chem. Eng. 2012, 1(4):380-395. Available at: http://linkinghub.elsevier.com/retrieve/pii/S2211339812000457
31. Flusberg B., Webster D.R., Lee J.H., Travers K.J., Olivares E.C., et al. Direct detection of DNA methylation during single-molecule, real-time sequencing. Nat. Methods 2010, 7(6):461-465.
32. Friedrich B., Schwartz E. Molecular biology of hydrogen utilization in aerobic chemolithotrophs. Annu. Rev. Microbiol. 1993, 47:351-383. Available at: http://www.ncbi.nlm.nih.gov/pubmed/8257102
33. Gerlitz M., Hrabak O., Schwab H. Partitioning of broad-host-range plasmid RP4 is a complex system involving site-specific recombination. J. Bacteriol. 1990, 172(11):6194-6203.
34. Gibson D.G., Young L., Chuang R., Venter J.C., Iii C.A.H., et al. Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat. Methods 2009, 6(5):12-16.
35. Golomysova A., Gomelsky M., Ivanov P.S. Flux balance analysis of photoheterotrophic growth of purple nonsulfur bacteria relevant to biohydrogen production. Int. J. Hydrog. Energy 2010, 35:12751-12760.
36. Grousseau E., Lu J., Gorret N., Guillouet S.E., Sinskey A.J. Isopropanol production with engineered Cupriavidus necator as bioproduction platform. Appl. Microbiol. Biotechnol. 2014, 98(9):4277-4290. Available at: http://www.ncbi.nlm.nih.gov/pubmed/24604499
37. Gruber S., Hagen J., Schwab H., Koefinger P. Versatile and stable vectors for efficient gene expression in Ralstonia eutropha H16. J. Biotechnol. 2014, 1-9. Available at: http://www.ncbi.nlm.nih.gov/pubmed/24998763
38. Guadalupe-Medina V., Wisselink H.W., Luttik M.A., De Hulster E., Daran J.-M., et al. Carbon dioxide fixation by Calvin-Cycle enzymes improves ethanol yield in yeast. Biotechnol. Biofuels 2013, 6(1):125. Available at: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3766054&tool=pmcentrez&rendertype=abstract
39. Hale C.R., Majumdar S., Elmore J., Pfister N., Compton M., et al. Essential features and rational design of CRISPR RNAs that function with the Cas RAMP module complex to cleave RNAs. Mol. Cell 2012, 45(3):292-302.
40. Hawkins A.S., McTernan P.M., Lian H., Kelly R.M., Adams M.W.W. Biological conversion of carbon dioxide and hydrogen into liquid fuels and industrial chemicals. Curr. Opin. Biotechnol. 2013, 24(3):376-384. Available at: http://www.sciencedirect.com/science/article/pii/S0958166913000311
41. Heap J.T., Pennington O.J., Cartman S.T., Minton N.P. A modular system for Clostridium shuttle plasmids. J. Microbiol. Methods 2009, 78(1):79-85.
42. Hu P., Rismani-Yazdi H., Stephanopoulos G. Anaerobic CO2 fixation by the acetogenic bacterium Moorella thermoacetica. AIChE J. 2013, 59(9):3176-3183. Available at: http://doi.wiley.com/10.1002/aic.14127
43. Hunter C.N., Daldal F., Thurnauer M.C., Beatty J.T. Advances in Photosynthesis and Respiration. Volume 28: The Purple Phototrophic Bacteria 2009, Springer, Dordrecht, The Netherlands, Available at: http://medcontent.metapress.com/index/A65RM03P4874243N.pdf
44. Ind A.C., Porter S.L., Brown M.T., Byles E.D., De Beyer J.A., et al. Inducible-expression plasmid for Rhodobacter sphaeroides and Paracoccus denitrificans. Appl. Environ. Microbiol. 2009, 75(20):6613-6615. Available at: http://www.ncbi.nlm.nih.gov/pubmed/19684165
45. Inui M., Nakata K., Roh J.H., Vertès A.A., Yukawa H. Isolation and molecular characterization of pMG160, a mobilizable cryptic plasmid from Rhodobacter blasticus. Appl. Environ. Microbiol. 2003, 69:725-733.
46. Iwasaki Y., Kita A., Sakai S., Takaoka K., Yano S., et al. Engineering of a functional thermostable kanamycin resistance marker for use in Moorella thermoacetica ATCC39073. FEMS Microbiol. Lett. 2013, 343(1):8-12.
47. Jaschke P.R., Saer R.G., Noll S., Beatty J.T. Modification of the Genome of Rhodobacter sphaeroides and Construction of Synthetic Operons 2011, Elsevier Inc., Available at: http://www.ncbi.nlm.nih.gov/pubmed/21601102 1st ed.
48. Jun D., Saer R.G., Madden J.D., Beatty J.T. Use of new strains of Rhodobacter sphaeroides and a modified simple culture medium to increase yield and facilitate purification of the reaction centre. Photosynth. Res. 2013, 1-9.
49. Kaserer H. Die oxydation des Wasserstoffes durch Mikroorganismen. Zent. Bakt. Part II 1906, 16:681.
50. Katzke N., Arvani S., Bergmann R., Circolone F., Markert A., et al. A novel T7 RNA polymerase dependent expression system for high-level protein production in the phototrophic bacterium Rhodobacter capsulatus. Protein Expr. Purif. 2010, 69(2):137-146. Available at: http://www.ncbi.nlm.nih.gov/pubmed/19706327
51. Keller M.W., Schut G.J., Lipscomb G.L., Menon A.L., Iwuchukwu I.J., et al. Exploiting microbial hyperthermophilicity to produce an industrial chemical, using hydrogen and carbon dioxide. Proc. Natl. Acad. Sci. USA 2013, 110(15):5840-5845. Available at: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3625313&tool=pmcentrez&rendertype=abstract
52. Khan N., Nybo S.E., Chappell J., Curtis W.R. Triterpene hydrocarbon production engineered into a metabolically versatile host - Rhodobacter capsulatus. Biotechnol. Bioeng. 2015, Available at: http://doi.wiley.com/10.1002/bit.25573
53. Khan N.E., Myers J.A., Tuerk A.L., Curtis W.R. A process economic assessment of hydrocarbon biofuels production using chemoautotrophic organisms. Bioresour. Technol. 2014, 172:201-211. Available at: http://www.sciencedirect.com/science/article/pii/S0960852414012346
54. Khunjar W.O., Sahin A., West A.C., Chandran K., Banta S. Biomass production from electricity using ammonia as an electron carrier in a reverse microbial fuel cell. PLoS One 2012, 7.
55. Kichise T., Fukui T., Yoshida Y., Doi Y. Biosynthesis of polyhydroxyalkanoates (PHA) by recombinant Ralstonia eutropha and effects of PHA synthase activity on in vivo PHA biosynthesis. Int. J. Biol. Macromol. 1999, 69-77.
56. Kiriukhin M., Tyurin M. Expression of amplified synthetic ethanol pathway integrated using Tn7-tool and powered at the expense of eliminated pta, ack, spo0A and spo0J during continuous syngas or CO2/H2 blend fermentation. J. Appl. Microbiol. 2013, 114(4):1033-1045. Available at: http://www.ncbi.nlm.nih.gov/pubmed/23289641
57. Kiriukhin M., Tyurin M. Mevalonate production by engineered acetogen biocatalyst during continuous fermentation of syngas or CO2/H2 blend. Bioprocess. Biosyst. Eng. 2014, 37(2):245-260. Available at: http://www.ncbi.nlm.nih.gov/pubmed/23775000
58. Kita A., Iwasaki Y., Sakai S., Okuto S., Takaoka K., et al. Development of genetic transformation and heterologous expression system in carboxydotrophic thermophilic acetogen Moorella thermoacetica. J. Biosci. Bioeng. 2012, 1-6.
59. Kontur W.S., Noguera D.R., Donohue T.J. Maximizing reductant flow into microbial H2 production. Curr. Opin. Biotechnol. 2012, 23(3):382-389. Available at: http://www.ncbi.nlm.nih.gov/pubmed/22036711
60. Köpke M., Held C., Hujer S., Liesegang H., Wiezer A., et al. Clostridium ljungdahlii represents a microbial production platform based on syngas. Proc. Natl. Acad. Sci. USA 2010, 107(29):13087-13092. Available at: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2919952&tool=pmcentrez&rendertype=abstract
61. Köpke M., Mihalcea C., Bromley J.C., Simpson S.D. Fermentative production of ethanol from carbon monoxide. Curr. Opin. Biotechnol. 2011, 22(3):320-325. Available at: http://www.ncbi.nlm.nih.gov/pubmed/21353524
62. Köpke M., Mihalcea C., Liew F., Tizard J.H., Ali M.S., et al. 2,3-Butanediol production by acetogenic bacteria, an alternative route to chemical synthesis, using industrial waste gas. Appl. Environ. Microbiol. 2011, 77(15):5467-5475. Available at: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3147483/
63. Kovach M.E., Elzer P.H., Hill D.S., Robertson G.T., Farris M.A., et al. Four new derivatives of the broad-host-range cloning vector pBBR1MCS, carrying different antibiotic-resistance cassettes. Gene 1995, 166(1):175-176. Available at: http://www.ncbi.nlm.nih.gov/pubmed/8529885
64. Kusian B., Bednarski R., Husemann M., Bowien B. Characterization of the duplicate ribulose-1,5-bisphosphate carboxylase genes and cbb promoters of Alcaligenes eutrophus. J. Bacteriol. 1995, 177:4442-4450.
65. LaBelle E.V., Marshall C.W., Gilbert J.A., May H.D. Influence of acidic pH on hydrogen and acetate production by an electrosynthetic microbiome. PLoS One 2014, 9:e109935. Available at: http://dx.plos.org/10.1371/journal.pone.0109935
66. Lawrence, J.G., Roth, J.R., 1996. Selfish Operons: Horizontal Transfer May Drive the Evolution of Gene Clusters.
67. Leang C., Ueki T., Nevin K.P., Lovley D.R. A genetic system for Clostridium ljungdahlii: a chassis for autotrophic production of biocommodities and a model homoacetogen. Appl. Environ. Microbiol. 2013, 79(4):1102-1109.
68. Lefebvre S., Lawson T., Fryer M., Zakhleniuk O.V, Lloyd J.C., et al. Increased sedoheptulose-1, 7-bisphosphatase activity in transgenic tobacco plants stimulates photosynthesis and growth from an early stage in development. Plant Physiol. 2005, 1(138):451-460.
69. Li H., Liao J.C. A synthetic anhydrotetracycline-controllable gene expression system in Ralstonia eutropha H16. ACS Synth. Biol. 2014, Available at: http://www.ncbi.nlm.nih.gov/pubmed/24702232
70. Li H., Opgenorth P.H., Wernick D.G., Rogers S., Wu T.-Y.T.-Y., et al. Integrated electromicrobial conversion of CO2 to higher alcohols. Science 2012, 335(6076):1596. Available at: http://www.sciencemag.org/cgi/doi/10.1126/science.1217643
71. Li X., Mercado R., Kernan T., West A.C., Banta S. Addition of citrate to Acidithiobacillus ferrooxidans cultures enables precipitate-free growth at elevated pH and reduces ferric inhibition. Biotechnol. Bioeng. 2014, 111(10):1940-1948. Available at: http://www.ncbi.nlm.nih.gov/pubmed/24771134
72. Liew F.M., Köpke M., Simpson S.D. Gas fermentation for commercial biofuels production. Liquid, Gaseous and Solid Biofuels - Conversion Techniques 2013, Z. Fang (Ed.).
73. Lovley D.R., Nevin K.P. Electrobiocommodities: powering microbial production of fuels and commodity chemicals from carbon dioxide with electricity. Curr. Opin. Biotechnol. 2013, 24(3):385-390. Available at: http://www.ncbi.nlm.nih.gov/pubmed/23465755
74. Lu J., Brigham C.J., Gai C.S., Sinskey A.J. Studies on the production of branched-chain alcohols in engineered Ralstonia eutropha. Appl. Microbiol. Biotechnol. 2012, 96:283-297.
75. Lubitz W., Ogata H., Rüdiger O., Reijerse E. Hydrogenases. Chem. Rev. 2014, 114(8):4081-4148. Available at: http://www.ncbi.nlm.nih.gov/pubmed/24655035
76. Lütte S., Pohlmann A., Zaychikov E., Schwartz E., Becher J.R., et al. Autotrophic production of stable-isotope-labeled arginine in Ralstonia eutropha strain H16. Appl. Environ. Microbiol. 2012, 78(22):7884-7890. Available at: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3485953&tool=pmcentrez&rendertype=abstract
77. Lutz R., Bujard H. Independent and tight regulation of transcriptional units in Escherichia coli via the LacR/O, the TetR/O and AraC/I1-I2 regulatory elements. Nucleic Acids Res. 1997, 25(6):1203-1210. Available at: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=146584&tool=pmcentrez&rendertype=abstract
78. Madigan M., Gest H. Growth of the photosynthetic bacterium Rhodopseudomonas capsulata chemoautotrophically in darkness with H2 as the energy source. J. Bacteriol. 1979, 137(1):524-530. Available at: http://jb.asm.org/content/137/1/524.short
79. Marshall C.W., Ross D.E., Fichot E.B., Norman R.S., May H.D. Long-term operation of microbial electrosynthesis systems improves acetate production by autotrophic microbiomes. Environ. Sci. Technol. 2013, 47(11):6023-6029.
80. Marx C.J., Lidstrom M.E. Broad-host-range cre-lox system for antibiotic marker recycling in Gram-negative bacteria. Biotechniques 2002, 33(5):1062-1067. Available at: http://www.ncbi.nlm.nih.gov/pubmed/12449384
81. Mather M.W., McReynolds L.M., Yu C.A. An enhanced broad-host-range vector for Gram-negative bacteria: avoiding tetracycline phototoxicity during the growth of photosynthetic bacteria. Gene 1995, 156:85-88.
82. Mattozzi M.D., Ziesack M., Voges M.J., Silver P.A., Way J.C. Expression of the sub-pathways of the Chloroflexus aurantiacus 3-hydroxypropionate carbon fixation bicycle in E. coli: toward horizontal transfer of autotrophic growth. Metab. Eng. 2013, 16:130-139. Available at: http://www.ncbi.nlm.nih.gov/pubmed/23376595
83. Mayer F., Müller V. Adaptations of anaerobic archaea to life under extreme energy limitation. FEMS Microbiol. Rev. 2014, 38(3):449-472.
84. Miyagawa Y., Tamoi M., Shigeoka S. Overexpression of a cyanobacterial fructose-1,6-/sedoheptulose-1,7-bisphosphatase in tobacco enhances photosynthesis and growth. Nat. Biotechnol. 2001, 19(10):965-969. Available at: http://www.ncbi.nlm.nih.gov/pubmed/11581664
85. Mueller-Cajar O., Whitney S.M. Directing the evolution of Rubisco and Rubisco activase: first impressions of a new tool for photosynthesis research. Photosynth. Res. 2008, 98(1-3):667-675. Available at: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2758363&tool=pmcentrez&rendertype=abstract
86. Müller J., MacEachran D., Burd H., Sathitsuksanoh N., Bi C., et al. Engineering of Ralstonia eutropha H16 for autotrophic and heterotrophic production of methyl ketones. Appl. Environ. Microbiol. 2013, 79(14):4433-4439. Available at: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3697500&tool=pmcentrez&rendertype=abstract
87. Murray I., Clark T., Morgan R.D., Boitano M., Anton B.P., et al. The methylomes of six bacteria. Nucleic Acids Res. 2012, 40(22):11450-11462.
88. Nagarajan H., Sahin M., Nogales J., Latif H., Lovley D.R., et al. Characterizing acetogenic metabolism using a genome-scale metabolic reconstruction of Clostridium ljungdahlii. Microb. Cell Fact. 2013, 12:118.
89. Nevin K.P., Hensley S.A., Franks A.E., Summers Z.M., Ou J., et al. Electrosynthesis of organic compounds from carbon dioxide is catalyzed by a diversity of acetogenic microorganisms. Appl. Environ. Microbiol. 2011, 77(9):2882-2886. Available at: http://aem.asm.org/content/77/9/2882.short
90. Nevin K.P., Woodard T.L., Franks A.E., Summers Z.M., Lovley D.R. Microbial electrosynthesis: feeding microbes electricity to convert carbon dioxide and water to multicarbon extracellular organic compounds. MBio 2010, 1(2):1-4. Available at: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2921159&tool=pmcentrez&rendertype=abstract
91. Niehaus T.D., Okada S., Devarenne T.P., Watt D.S., Sviripa V., et al. Identification of unique mechanisms for triterpene biosynthesis in Botryococcus braunii. Proc. Natl. Acad. Sci. USA 2011, 108(30):12260-12265. Available at: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3145686&tool=pmcentrez&rendertype=abstract
92. Paoli G.C., Tabita F.R. Aerobic chemolithoautotrophic growth and RubisCO function in Rhodobacter capsulatus and a spontaneous gain of function mutant of Rhodobacter sphaeroides. Arch. Microbiol. 1998, 170(1):8-17. Available at: http://www.ncbi.nlm.nih.gov/pubmed/9639598
93. Park J.M., Kim T.Y., Lee S.Y. Genome-scale reconstruction and in silico analysis of the Ralstonia eutropha H16 for polyhydroxyalkanoate synthesis, lithoautotrophic growth, and 2-methyl citric acid production. BMC Syst. Biol. 2011, 5(1):101. Available at: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3154180&tool=pmcentrez&rendertype=abstract
94. Phillips J.R., Clausen E.C., Gaddy J.L. Synthesis gas as substrate for the biological production of fuels and chemicals. Appl. Biochem. Biotechnol. 1994, 45-46:145-157.
95. Phillips J.R., Klasson K.T., Clausen E.C., Gaddy J.L. Biological production of ethanol from coal synthesis gas. Appl. Biochem. Biotechnol. 1993, 39-40(1):559-571. Available at: http://www.springerlink.com/index/10.1007/BF02919018
96. Quandt J., Hynes M.F. Versatile suicide vectors which allow direct selection for gene replacement in Gram-negative bacteria. Gene 1993, 127(1):15-21. Available at: http://linkinghub.elsevier.com/retrieve/pii/0378111993906116
97. Rabaey K., Rozendal R.A. Microbial electrosynthesis - revisiting the electrical route for microbial production. Nat. Rev. Microbiol. 2010, 8(10):706-716. Available at: http://dx.doi.org/10.1038/nrmicro2422
98. Rocha E.P.C., Cornet E., Michel B. Comparative and evolutionary analysis of the bacterial homologous recombination systems. PLoS Genet. 2005, 1(2):e15.
99. Rohwerder T., Müller R.H. Biosynthesis of 2-hydroxyisobutyric acid (2-HIBA) from renewable carbon. Microb. Cell Fact. 2010, 9:13.
100. Rousset M., Liebgott P. Engineering hydrogenases for H2 production: bolts and goals. Microbial BioEnergy: Hydrogen Production. Advances in Photosynthesis and Respiration. Dordrecht 2014, 43-77. Springer, Netherlands, Available at: http://link.springer.com/10.1007/978-94-017-8554-9 D. Zannoni, R. De Philippis (Eds.).
101. Rozendal R.A., Jeremiasse A.W., Hamelers H.V.M., Buisman C.J.N. Hydrogen Production with a microbial biocathode. Environ. Sci. Technol. 2008, 42(2):629-634.
102. Ryu H., Hahn S., Chang Y.K., Chang H.N. Production of poly(3-hydroxybutyrate) by high cell density fed-batch culture of Alcaligenes eutrophus with phospate limitation. Biotechnology 1997, 5(1):28-32. Available at: http://onlinelibrary.wiley.com/doi/10.1002/(SICI)1097-0290(19970705)55:1 28::AID-BIT4 3.0.CO;2-Z/abstract
103. Sato S., Fujiki T., Matsumoto K. Construction of a stable plasmid vector for industrial production of poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) by a recombinant Cupriavidus necator H16 strain. J. Biosci. Bioeng. 2013, 116(6):677-681. Available at: http://www.ncbi.nlm.nih.gov/pubmed/23816763
104. Schick M., Xie X., Ataka K., Kahnt J., Linne U., et al. Biosynthesis of the iron-guanylylpyridinol cofactor of [Fe]-hydrogenase in methanogenic archaea as elucidated by stable-isotope labeling. J. Am. Chem. Soc. 2012, 134(6):3271-3280.
105. Schiel-Bengelsdorf B., Dürre P. Pathway engineering and synthetic biology using acetogens. FEBS Lett. 2012, 586(15):2191-2198. Available at: http://www.ncbi.nlm.nih.gov/pubmed/22710156
106. Schwartz E., Fritsch J., Friedrich B. H2-metabolizing prokaryotes. The Prokaryotes - Prokaryotic Physiology and Biochemistry 2013, 119-199. Springer Berlin Heidelberg, Berlin, Heidelberg, Available at: http://link.springer.com/10.1007/978-3-642-30141-4 E. Rosenberg, E.F. DeLong, S. Lory, E. Stackebrandt, F. Thompson (Eds.).
107. Shively J.M., Keulen G., Van, Meijer W.G. SOMETHING FROM ALMOST NOTHING: carbon dioxide fixation in chemoautotrophs occurrence in bacteria. Biotechnology 1998, 191-230.
108. Siegel R.S., Ollis D.F. Kinetics of growth of the hydrogen-oxidizing bacterium Alcaligenes eutrophus (ATCC 17707) in chemostat culture. Biotechnol. Bioeng. 1984, 26(7):764-770. Available at: http://www.ncbi.nlm.nih.gov/pubmed/18553444
109. Smith S., Tabita F.R. Positive and negative selection of mutant forms of prokaryotic (Cyanobacterial) ribulose-1,5-bisphosphate carboxylase/oxygenase. J. Mol. Biol. 2003, 331(3):557-569. Available at: http://linkinghub.elsevier.com/retrieve/pii/S0022283603007861
110. Solaiman D.K.Y., Swingle B.M., Ashby R.D. A new shuttle vector for gene expression in biopolymer-producing Ralstonia eutropha. J. Microbiol. Methods 2010, 82:120-123.
111. Straub M., Demler M., Weuster-Botz D., Dürre P. Selective enhancement of autotrophic acetate production with genetically modified Acetobacterium woodii. J. Biotechnol. 2014, 67-72. Available at: http://www.sciencedirect.com/science/article/pii/S0168165614001084#
112. Sun J., Alper H.S. Metabolic engineering of strains: from industrial-scale to lab-scale chemical production. J. Ind. Microbiol. Biotechnol. 2014, 42:423-436. Available at: http://link.springer.com/10.1007/s10295-014-1539-8
113. Suzuki T., Yasui K. Plasmid artificial modification: a novel method for efficient DNA transfer into bacteria. Plasmid 2011, 765. J.A. Williams (Ed.).
114. Sydow A., Krieg T., Mayer F., Schrader J., Holtmann D. Electroactive bacteria - molecular mechanisms and genetic tools. Appl. Microbiol. Biotechnol. 2014, 98(20):8481-8495. Available at: http://www.ncbi.nlm.nih.gov/pubmed/25139447
115. Tanaka K., Ishizaki A., Kanamaru T., Kawano T. Production of poly (D-3-hydroxybutyrate) from CO2, H2, and O2 by high cell density autotrophic cultivation of Alcaligenes eutrophus. Biotechnol. Bioeng. 1995, 45(3):268-275. Available at: http://onlinelibrary.wiley.com/doi/10.1002/bit.260450312/abstract
116. Thauer R.K., Kaster A.-K., Seedorf H., Buckel W., Hedderich R. Methanogenic archaea: ecologically relevant differences in energy conservation. Nat. Rev. Microbiol. 2008, 6(8):579-591. Available at: http://www.ncbi.nlm.nih.gov/pubmed/18587410
117. Tikh I.B., Held M., Schmidt-Dannert C. BioBrick(TM) compatible vector system for protein expression in Rhodobacter sphaeroides. Appl. Microbiol. Biotechnol. 2014, 98(7):3111-3119.
118. Tsukahara K., Kita A., Nakashimada Y., Hoshino T., Murakami K. Genome-guided analysis of transformation efficiency and carbon dioxide assimilation by Moorella thermoacetica Y72. Gene 2014, 535(2):150-155.
119. Ueki T., Nevin K.P., Woodard T.L., Lovley D.R. Converting carbon dioxide to butyrate with an engineered strain of Clostridium ljungdahlii. MBio 2014, 5(5):19-23. Available at: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4212834/
120. Umeda F., Min H., Urushihara M., Okazaki M., Miura Y. Conjugal transfer of hydrogen-oxidizing ability of Alcaligenes hydrogenphilus to Pseudomonas oxalatus. Biochem. Biophys. Res. Commun. 1986, 137(1):108-113. Available at: http://www.sciencedirect.com/science/article/pii/000629186911824#
121. Veit A., Akhtar M.K., Mizutani T., Jones P.R. Constructing and testing the thermodynamic limits of synthetic NAD(P)H:H2 pathways. Microb. Biotechnol 2008, 1(5):382-394. Available at: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3815245&tool=pmcentrez&rendertype=abstract
122. Vignais P.M., Billoud B. Occurrence, classification, and biological function of hydrogenases: an overview. Chem. Rev. 2007, 107(10):4206-4272. Available at: http://www.ncbi.nlm.nih.gov/pubmed/17927159
123. Villano M., Aulenta F., Ciucci C., Ferri T., Giuliano A., et al. Bioelectrochemical reduction of CO(2) to CH(4) via direct and indirect extracellular electron transfer by a hydrogenophilic methanogenic culture. Bioresour. Technol 2010, 101(9):3085-3090.
124. Volova T.G., Kalacheva G.S., Altukhova O.V. Autotrophic synthesis of polyhydroxyalkanoates by the bacteria Ralstonia eutropha in the presence of carbon monoxide. Appl. Microbiol. Biotechnol. 2002, 58:675-678. Available at: http://link.springer.com/article/10.1007%2Fs00253-002-0941-8
125. Voss I., Steinbüchel A. Application of a KDPG-aldolase gene-dependent addiction system for enhanced production of cyanophycin in Ralstonia eutropha strain H16. Metab. Eng. 2006, 8(1):66-78. Available at: http://www.ncbi.nlm.nih.gov/pubmed/16266816
126. Wang F., Lee S.Y. Poly(3-Hydroxybutyrate) production with high productivity and high polymer content by a fed-batch culture of Alcaligenes latus under nitrogen limitation. Appl. Environ. Microbiol. 1997, 63(9):3703-3706. Available at: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1389255&tool=pmcentrez&rendertype=abstract
127. Whitney S.M., Houtz R.L., Alonso H. Advancing our understanding and capacity to engineer nature's CO2-sequestering enzyme, Rubisco. Plant Physiol. 2011, 155(1):27-35. Available at: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3075749&tool=pmcentrez&rendertype=abstract
128. Yagi K., Min H., Urushihara M., Manabe Y., Umeda F., et al. Isolation of hydrogen-oxidation gene from Alcaligenes hydrogenophilus and its expression in Pseudomonas oxalaticus. Biochem. Biophys. Res. Commun. 1986, 1:114-119. Available at: http://www.sciencedirect.com/science/article/pii/000629186911836
129. Yasui K., Kano Y., Tanaka K., Watanabe K., Shimizu-Kadota M., et al. Improvement of bacterial transformation efficiency using plasmid artificial modification. Nucleic Acids Res. 2009, 37(1):e3.