Production of fatty acids in Ralstonia eutropha H16 by engineering β-oxidation and carbon storage

PeerJ

Volumn 2015, Issue 12, 2015, Pages

  Chen, Janice S ^a,b   Colón, Brendan ^a   Dusel, Brendon ^a   Ziesack, Marika ^a   Way, Jeffrey C ^a   Torella, Joseph P ^a  

^a HARVARD MEDICAL SCHOOL   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Acyl CoA ligase; Biofuel; Metabolic engineering; Ralstonia; oxidation

Indexed keywords

FATTY ACID;

ARTICLE; CUPRIAVIDUS NECATOR; DOWNSTREAM PROCESSING; ENGINEERING; FATTY ACID OXIDATION; GENE EXPRESSION; NONHUMAN; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS; SPECTROPHOTOMETRY;

EID: 84951038187     PISSN: None     EISSN: 21678359     Source Type: Journal    
DOI: 10.7717/peerj.1468     Document Type: Article

References (37)

1. Akhtar MK, Turner NJ, Jones PR. 2013. Carboxylic acid reductase is a versatile enzyme for the conversion of fatty acids into fuels and chemical commodities. Proceedings of the National Academy of Sciences of the United States of America 110:87-92 DOI 10.1073/pnas.1216516110.
2. Bi C, Su P, Muller J, Yeh Y-C, Chhabra S, Beller H, Singer S, Hillson N. 2013. Development of a broad-host synthetic biology toolbox for Ralstonia eutropha and its application to engineering hydrocarbon biofuel production. Microbial Cell Factories 12:107 DOI 10.1186/1475-2859-12-107.
3. Brigham CJ, Budde CF, Holder JW, Zeng Q, Mahan AE, Rha C, Sinskey AJ. 2010. Elucidation of beta-oxidation pathways in Ralstonia eutropha H16 by examination of global gene expression. Journal of Bacteriology 192:5454-5464 DOI 10.1128/JB.00493-10.
4. Bullard JH, PurdomE, Hansen KD, Dudoit S. 2010. Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. BMC Bioinformatics 11:94 DOI 10.1186/1471-2105-11-94.
5. Chung AL, Jin HL, Huang LJ, Ye HM, Chen JC, Wu Q, Chen GQ. 2011. Biosynthesis and characterization of poly(3-hydroxydodecanoate) by ß-oxidation inhibited mutant of pseudomonas entomophila L48. Biomacromolecules 12:3559-3566 DOI 10.1021/bm200770m.
6. Cook A, Schlegel H. 1978. Metabolite concentrations in Alcaligenes eutrophus H 16 and a mutant defective in poly-ß-hydroxybutyrate synthesis. Archives of Microbiology 119:231-235 DOI 10.1007/BF00405400.
7. Dellomonaco C, Clomburg JM, Miller EN, Gonzalez R. 2011. Engineered reversal of the beta-oxidation cycle for the synthesis of fuels and chemicals. Nature 476:355-359 DOI 10.1038/nature10333.
8. Farewell A, Diez AA, DiRusso CC, NystromT. 1996. Role of the Escherichia coli FadR regulator in stasis survival and growth phase-dependent expression of the uspA, fad, and fab genes. Journal of Bacteriology 178:6443-6450.
9. Grousseau E, Lu J, Gorret N, Guillouet SE, Sinskey AJ. 2014. Isopropanol production with engineered Cupriavidus necator as bioproduction platform. Applied Microbiology and Biotechnology 98:4277-4290 DOI 10.1007/s00253-014-5591-0.
10. Henderson RA, Jones CW. 1997. Physiology of poly-3-hydroxybutyrate (PHB) production by Alcaligenes eutrophus growing in continuous culture. Microbiology 143:2361-2371 DOI 10.1099/00221287-143-7-2361.
11. Insomphun C, Mifune J, Orita I, Numata K, Nakamura S, Fukui T. 2014. Modification of beta-oxidation pathway in Ralstonia eutropha for production of poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) from soybean oil. Journal of Bioscience and Bioengineering 117:184-190 DOI 10.1016/j.jbiosc.2013.07.016.
12. Kuhl KP, Cave ER, Abram DN, Jaramillo TF. 2012. New insights into the electrochemical reduction of carbon dioxide on metallic copper surfaces. Energy & Environmental Science 5:7050-7059 DOI 10.1039/c2ee21234j.
13. Lageveen RG, Huisman GW, Preusting H, Ketelaar P, Eggink G, Witholt B. 1988. Formation of polyesters by pseudomonas oleovorans: effect of substrates on formation and composition of poly-(R)-3-hydroxyalkanoates and poly-(R)-3-hydroxyalkenoates. Applied and Environmental Microbiology 54:2924-2932.
14. Lennen RM, Pfleger BF. 2013. Microbial production of fatty acid-derived fuels and chemicals. Current Opinion in Biotechnology 24:1044-1053 DOI 10.1016/j.copbio.2013.02.028.
15. Li H, Opgenorth PH, Wernick DG, Rogers S, Wu TY, Higashide W, Malati P, Huo YX, Cho KM, Liao JC. 2012. Integrated electromicrobial conversion of CO2 to higher alcohols. Science 335:1596 DOI 10.1126/science.1217643.
16. Liu Q, Luo G, Zhou XR, Chen GQ. 2011. Biosynthesis of poly(3-hydroxydecanoate) and 3-hydroxydodecanoate dominating polyhydroxyalkanoates by ß-oxidation pathway inhibited pseudomonas putida. Metabolic Engineering 13:11-17 DOI 10.1016/j.ymben.2010.10.004.
17. Lu J, Brigham CJ, Gai CS, Sinskey AJ. 2012. Studies on the production of branched-chain alcohols in engineered Ralstonia eutropha. Applied Microbiology and Biotechnology 96:283-297 DOI 10.1007/s00253-012-4320-9.
18. Lu X, Vora H, Khosla C. 2008. Overproduction of free fatty acids in E. coli: implications for biodiesel production. Metabolic Engineering 10:333-339 DOI 10.1016/j.ymben.2008.08.006.
19. McClure R, Balasubramanian D, Sun Y, Bobrovskyy M, Sumby P, Genco CA, Vanderpool CK, Tjaden B. 2013. Computational analysis of bacterial RNA-Seq data. Nucleic Acids Research 41:e140 DOI 10.1093/nar/gkt444.
20. Muller J, MacEachran D, Burd H, Sathitsuksanoh N, Bi C, Yeh YC, Lee TS, Hillson NJ, Chhabra SR, Singer SW, Beller HR. 2013. Engineering of Ralstonia eutropha H16 for autotrophic and heterotrophic production of methyl ketones. Applied and Environmental Microbiology 79:4433-4439 DOI 10.1128/AEM.00973-13.
21. Nevin KP, Woodard TL, Franks AE, Summers ZM, Lovley DR. 2010. Microbial electrosynthesis: feeding microbes electricity to convert carbon dioxide and water to multicarbon extracellular organic compounds. MBio 1 e00103-e00110 DOI 10.1128/mBio.00103-10.
22. Nomura CT, Tanaka T, Gan Z, Kuwabara K, Abe H, Takase K, Taguchi K, Doi Y. 2004. Effective enhancement of short-chain-length-medium-chain-length polyhydroxyalkanoate copolymer production by coexpression of genetically engineered 3-ketoacyl-acyl-carrier-protein synthase III (fabH) and polyhydroxyalkanoate synthesis genes. Biomacromolecules 5:1457-1464 DOI 10.1021/bm049959v.
23. Pohlmann A, Fricke WF, Reinecke F, Kusian B, Liesegang H, Cramm R, Eitinger T, Ewering C, Potter M, Schwartz E, Strittmatter A, Voss I, Gottschalk G, Steinbuchel A, Friedrich B, Bowien B. 2006. Genome sequence of the bioplastic-producing "Knallgas" bacterium Ralstonia eutropha H16. Nature Biotechnology 24:1257-1262 DOI 10.1038/nbt1244.
24. Rabaey K, Butzer S, Brown S, Keller J, Rozendal RA. 2010. High current generation coupled to caustic production using a lamellar bioelectrochemical system. Environmental Science and Technology 44:4315-4321 DOI 10.1021/es9037963.
25. Runguphan W, Keasling JD. 2014. Metabolic engineering of Saccharomyces cerevisiae for production of fatty acid-derived biofuels and chemicals. Metabolic Engineering 21:103-113 DOI 10.1016/j.ymben.2013.07.003.
26. Salis HM, Mirsky EA, Voigt CA. 2009. Automated design of synthetic ribosome binding sites to control protein expression. Nature Biotechnology 27:946-950 DOI 10.1038/nbt.1568.
27. Schlegel HG, Lafferty R. 1965. Growth of/'Knallgas/' bacteria (Hydrogenomonas) using direct electrolysis of the culture medium. Nature 205:308-309 DOI 10.1038/205308b0.
28. Shimizu R, Chou K, Orita I, Suzuki Y, Nakamura S, Fukui T. 2013. Detection of phase-dependent transcriptomic changes and Rubisco-mediated CO2 fixation into poly (3-hydroxybutyrate) under heterotrophic condition in Ralstonia eutropha H16 based on RNA-seq and gene deletion analyses. BMC Microbiology 13:169 DOI 10.1186/1471-2180-13-169.
29. Steen EJ, Kang Y, Bokinsky G, Hu Z, Schirmer A, McClure A, Del Cardayre SB, Keasling JD. 2010. Microbial production of fatty-acid-derived fuels and chemicals from plant biomass. Nature 463:559-562 DOI 10.1038/nature08721.
30. Torella JP, Ford TJ, Kim SN, Chen AM, Way JC, Silver PA. 2013. Tailored fatty acid synthesis via dynamic control of fatty acid elongation. Proceedings of the National Academy of Sciences of the United States of America 110:11290-11295 DOI 10.1073/pnas.1307129110.
31. Torella JP, Gagliardi CJ, Chen JS, Bediako DK, Colon B, Way JC, Silver PA, Nocera DG. 2015. Efficient solar-to-fuels production from a hybrid microbial-water-splitting catalyst system. Proceedings of the National Academy of Sciences of the United States of America 112:2337-2342 DOI 10.1073/pnas.1424872112.
32. Tsuge T, Yano K, Imazu S-I, Numata K, Kikkawa Y, Abe H, Taguchi S, Doi Y. 2005. Biosynthesis of polyhydroxyalkanoate (PHA) copolymer from fructose using wild-type and laboratoryevolved PHA synthases. Macromolecular Bioscience 5:112-117 DOI 10.1002/mabi.200400152.
33. Verlinden RA, Hill DJ, Kenward MA, Williams CD, Radecka I. 2007. Bacterial synthesis of biodegradable polyhydroxyalkanoates. Journal of Applied Microbiology 102:1437-1449 DOI 10.1111/j.1365-2672.2007.03335.x.
34. Voelker TA, Davies HM. 1994. Alteration of the specificity and regulation of fatty acid synthesis of Escherichia coli by expression of a plant medium-chain acyl-acyl carrier protein thioesterase. Journal of Bacteriology 176:7320-7327.
35. Wang J, Yu HQ. 2007. Biosynthesis of polyhydroxybutyrate (PHB) and extracellular polymeric substances (EPS) by Ralstonia eutropha ATCC 17699 in batch cultures. Applied Microbiology and Biotechnology 75:871-878 DOI 10.1007/s00253-007-0870-7.
36. Kovach ME, Elzer PH, Hill DS, Robertson GT, Farris MA, Roop 2nd RM, Peterson KM. 1995. Four new derivatives of the broad-host-range cloning vector pBBR1MCS, carrying different antibiotic-resistance cassettes. Gene 166:175-176 DOI 10.1016/0378-1119(95)00584-1.
37. Simon R, Priefer U, Puhler A. 1983. A broad host range mobilization system for in vivo genetic engineering: transposon mutagenesis in gram negative bacteria. Nature Biotechnology 1:784-791 DOI 10.1038/nbt1183-784.