Skip to main content
SpringerLink
Log in

Synthetic Biology and Future Production of Biofuels and High–Value Products

  • Chapter
  • First Online:
Climate Change, Photosynthesis and Advanced Biofuels

Abstract

Synthetic biology aims to build increasingly complex biological systems from standard interchangeable parts. The ideal microorganism for biofuel production may produce a single fermentation product and might possess high substrate utilization and processing capacities. Such microorganisms may also possess fast and deregulated pathways for sugar transport, good tolerance to inhibitors and product, and high metabolic fluxes. The choice to produce such an organism lies between engineering natural function and importing biosynthetic capacity which is affected by current progress in metabolic engineering and synthetic biology. Synthetic biology is bringing together engineers and biologists to design and build novel biomolecular components, networks, and pathways and to use these constructs to rewire and reprogram organisms. Recent findings that plant metabolic pathways can be reconstituted in heterologous hosts and metabolism in crop plants can be engineered to improve the production of biofuels have given new hope for molecular biological approaches in improving food and biofuel production. The de novo engineering of genetic circuits, biological modules, and synthetic pathways is beginning to address these crucial problems and is being used in related practical applications.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 189.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 249.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 249.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Agostini F, Voller J-S, Koksch B, Acevedo-Rocha CG, Kubyshkin V, Budisa N (2017) Xenobiology meets enzymology: exploring the potential of unnatural building blocks in biocatalysis. Angew Chem Int Ed Engl. https://doi.org/10.1002/anie.201610129. [Epub ahead of print]

  • Alper H, Stephanopoulos G (2009) Engineering for biofuels: exploiting innate microbial capacity or importing biosynthetic potential. Nat Rev Microbiol 7:715–723

    CAS  PubMed  Google Scholar 

  • Angermayr SA, Hellingwerf KJ, Lindblad P, de Mattos MJ (2009) Energy biotechnology with cyanobacteria. Curr Opin Biotechnol 20:257–263

    CAS  PubMed  Google Scholar 

  • Arslan D, Steinbusch KJJ, Diels L, De Wever H, Buisman CJN, Hamelers HVM (2012) Effect of hydrogen and carbon dioxide on carboxylic acids patterns in mixed culture fermentation. Bioresour Technol 118:227–234

    CAS  PubMed  Google Scholar 

  • Atsumi S, Hanai T, Liao JC (2008a) Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels. Nature 451:86–89

    CAS  PubMed  Google Scholar 

  • Atsumi S, Canna AF, Connora MR, Shena CR, Smitha KM, Brynildsena MP, Choua KJY, Hanai T, Liao JC (2008b) Metabolic engineering of Escherichia coli for 1-butanol production. Metab Eng 10(6):305–311. https://doi.org/10.1016/j.ymben.2007.08.003

    Article  CAS  PubMed  Google Scholar 

  • Babu RP, O’Connor KO, Seeram R (2013) Current progress on bio-based polymers and their future trends. Prog Biomater 2:1–16

    Google Scholar 

  • Barber J (2009) Photosynthetic energy conversion: natural and artificial. Chem Soc Rev 38:185–196

    CAS  PubMed  Google Scholar 

  • Becker J, Wittmann C (2016) Systems metabolic engineering of Escherichia coli for the heterologous production of high value molecules a veteran at new shores. Curr Opin Biotechnol 42:178–188. https://doi.org/10.1016/j.copbio.2016.05.004

    Article  CAS  PubMed  Google Scholar 

  • Beckers V, Castro IP, Tomasch J, Wittmann C (2016) Integrated analysis of gene expression and metabolic fluxes in PHA—producing Pseudomonas putida grown on glycerol. Microb Cell Factories 15:73

    Google Scholar 

  • Beerthuis R, Rothenber G, Shiju NR (2015) Catalytic routes towards acrylic acid, adipic acid, and ε-caprolactam starting from biorenewables. Green Chem 17:1341–1361

    CAS  Google Scholar 

  • Behler J, Vijay D, Hess WR, Akhtar MK (2018) CRISPR-based technologies for metabolic engineering in cyanobacteria. Trends Biotechnol 36(10):996–1010. https://doi.org/10.1016/j.tibtech.2018.05.011

    Article  CAS  PubMed  Google Scholar 

  • Beller HR, Lee TS, Katz L (2015) Natural products as biofuels and bio-based chemicals: fatty acids and isoprenoids. Nat Prod Rep 32:1508–1526

    CAS  PubMed  Google Scholar 

  • Bhansali S, Kumar A (2018) Synthetic and semisynthetic metabolic pathways for biofuel production. In: Kumar A, Ogita S, Yau Y-Y (eds) Biofuels: greenhouse gas mitigation and global warming, Next generation biofuels and role of biotechnology. Springer, Heidelberg, pp 421–432

    Google Scholar 

  • Birgen C, Dürre P, Preisig HA, Wentzel A (2019) Butanol production from lignocellulosic biomass: revisiting fermentation performance indicators with exploratory data analysis. Biotechnol Biofuels 12:167. https://doi.org/10.1186/s13068-019-1508-6

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Brock JT, Freedman AJE, Tompsett GA, Muse SK, Allen AJ, Jackson LA, Thompson JR (2019) Engineered microbial biofuel production and recovery under supercritical carbon dioxide. Nat Commun 10(1):587. https://doi.org/10.1038/s41467-019-08486-6

    Article  CAS  Google Scholar 

  • Campos-Fernández J, Arnal JM, Gómez J, Dorado MP (2012) A comparison of performance of higher alcohols/diesel fuel blends in a diesel engine. Appl Energy 95:267–275

    Google Scholar 

  • Carroll A, Somerville C (2009) Cellulosic biofuels. Annu Rev Plant Biol 60:165–182

    CAS  PubMed  Google Scholar 

  • Case AE, Atsumi S (2016) Cyanobacterial chemical production. J Biotechnol 231:106–114

    CAS  PubMed  Google Scholar 

  • Chae TU, Choi SY, Kim JW, Ko Y (2017) Science direct recent advances in systems metabolic engineering tools and strategies. Curr Opin Biotechnol 47:67–82. https://doi.org/10.1016/j.copbio.2017.06.007

    Article  CAS  PubMed  Google Scholar 

  • Chakravorty U, Hubert M, Nostbakken L (2009) Fuel versus food. Annu Rev Res Econ 1:645–663. https://doi.org/10.1146/annurev.resource.050708.144200

    Article  Google Scholar 

  • Chen J, Sun S, Li C-Z, Zhu Y-G, Rosen BP (2014) Biosensor for organoarsenical herbicides and growth promoters. Environ Sci Technol 48:1141–1147

    CAS  PubMed  PubMed Central  Google Scholar 

  • Christianson DW (2008) Unearthing the roots of the terpenome. Curr Opin Chem Biol 12(2):141–150

    CAS  PubMed  PubMed Central  Google Scholar 

  • Cirino PC, Tang Y, Takahashi K, Tirrell DA, Arnold FH (2003) Global incorporation of norleucine in place of methionine in cytochrome P450 BM-3 heme domain increases peroxygenase activity. Biotechnol Bioeng 83:729–734

    CAS  PubMed  Google Scholar 

  • Claypool JT, Ramon DR (2013) Development and validation of a technoeconomic analysis tool for early-stage evaluation of bio-based chemical production processes. Bioresour Technol 150:486–495

    CAS  PubMed  Google Scholar 

  • Claypool JT, Ramon DR, Jarboe LR, Nielsen DR (2014) Technoeconomic evaluation of bio-based styrene production by engineered Escherichia coli. J Ind Microbiol Biotechnol 2014(41):1211–1216

    Google Scholar 

  • Clomburg JM, Blankschien MD, Vick JE, Chou A, Kim S, Gonzalez R (2015) Integrated engineering of b-oxidation reversal and v-oxidation pathways for the synthesis of medium chain v-functionalized carboxylic acids. Metab Eng 28:202–212

    CAS  PubMed  Google Scholar 

  • Cobb RE, Wang Y, Zhao H (2015) High-efficiency multiplex genome editing of Streptomyces species using an engineered CRISPR/Cas system. ACS Synth Biol 4:723–728

    CAS  PubMed  Google Scholar 

  • Connor MR, Atsumi S (2010) Synthetic biology guides biofuel production. J Biomed Biotechnol 2010:1–9

    Google Scholar 

  • Conrado RJ, Gonzalez R (2014) Chemistry. Envisioning the bioconversion of methane to liquid fuels. Science 343:621–623

    CAS  PubMed  Google Scholar 

  • Couto JM, Mcgarrity A, Russell J, Sloan WT (2018) The effect of metabolic stress on genome stability of a synthetic biology chassis Escherichia coli K12 strain. Microb Cell Factories 17:1–10. https://doi.org/10.1186/s12934-018-0858-2

    Article  Google Scholar 

  • Dai Z, Nielsen J (2015) Advancing metabolic engineering through systems biology of industrial microorganisms. Curr Opin Biotechnol 36:8–15

    PubMed  Google Scholar 

  • Diao L, Liu Y, Qian F, Yang J, Jiang Y, Yang S (2013) Construction of fast xylose-fermenting yeast based on industrial ethanol-producing diploid Saccharomyces cerevisiae by rational design and adaptive evolution. BMC Biotechnol 13:110

    PubMed  PubMed Central  Google Scholar 

  • DiCarlo JE, Norville JE, Mali P, Rios X, Aach J, Church GM (2013) Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems. Nucleic Acids Res 41:4336–4343

    CAS  PubMed  PubMed Central  Google Scholar 

  • Dismukes GC, Carrieri D, Bennette N, Ananyev GM, Posewitz MC (2008) Aquatic phototrophs: efficient alternatives to land-based crops for biofuels. Curr Opin Biotechnol 19:235–240

    CAS  PubMed  Google Scholar 

  • Dueber JE et al (2009) Synthetic protein scaffolds provide modular control over metabolic flux. Nat Biotechnol 27(8):753–759

    CAS  PubMed  Google Scholar 

  • Earhart AJJF, Forijj APC, Patel MK (2012) Replacing fossil based PET with biobased PEF: process analysis, energy and GHG balance. Energy Environ Sci 5:6407–6422

    Google Scholar 

  • Erb TJ, Zarzycki J (2016) Biochemical and synthetic biology approaches to improve photosynthetic CO2-fixation. Curr Opin Chem Biol 34:72–79

    CAS  PubMed  PubMed Central  Google Scholar 

  • Espaux L, Mendez-perez D, Li R, Keasling JD (2015) Synthetic biology for microbial production of lipid-based biofuels. Curr Opin Chem Biol 29:58–65. https://doi.org/10.1016/j.cbpa.2015.09.009

    Article  CAS  PubMed  Google Scholar 

  • Estrela R, Cate JHD (2016) Energy biotechnology in the CRISPR-Cas9 era. Curr Opin Biotechnol 38:79–84. https://doi.org/10.1016/j.copbio.2016.01.005

    Article  CAS  PubMed  Google Scholar 

  • Farr G, Blancquaert D, Capell T, Van Der Straeten D, Christou P, Zhu C (2014) Engineering complex metabolic pathways in plants. Annu Rev Plant Biol 65:187–223. https://doi.org/10.1146/annurev-arplant-050213-035825

    Article  CAS  Google Scholar 

  • Fei Q, Guarnieri MT, Tao L, Laurens LM, Dowe N, Pienkos PT (2014) Bioconversion of natural gas to liquid fuel: opportunities and challenges. Biotechnol Adv 32:596–614

    CAS  PubMed  Google Scholar 

  • Feng X, Lian J, Zhao H (2014) Metabolic engineering of Saccharomyces cerevisiae to improve 1-hexadecanol production. Metab Eng 27:10–19

    PubMed  Google Scholar 

  • Fortman JL et al (2008) Biofuel alternatives to ethanol: pumping the microbial well. Trends Biotechnol 26:375–381

    CAS  PubMed  Google Scholar 

  • French KE (2019) Harnessing synthetic biology for sustainable development. Nat Sustain 2:250–252

    Google Scholar 

  • Gaida SM, Liedtke A, Heinz A, Jentges W, Engels B, Jennewein S (2016) Metabolic engineering of Clostridium cellulolyticum for the production of n-butanol from crystalline cellulose. Microb Cell Fact 15:6. https://doi.org/10.1186/s12934-015-0406-2

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gall DL, Ralph J, Donohue TJ, Noguera DR (2017) Biochemical transformation of lignin for deriving valued commodities from lignocellulose. Curr Opin Biotechnol 45:120–126. https://doi.org/10.1016/j.copbio.2017.02.015

    Article  CAS  PubMed  Google Scholar 

  • Georgianna DR, Stephen P (2012) Exploiting diversity and synthetic biology for the production of algal biofuels. Nature 488:330–335. https://doi.org/10.1038/nature11479

    Article  CAS  Google Scholar 

  • Giessen TW, Silver PA (2017) Engineering carbon fixation with artificial protein organelles. Curr Opin Biotechnol 46:42–50. https://doi.org/10.1016/j.copbio.2017.01.004

    Article  CAS  PubMed  Google Scholar 

  • Goh E-B, Baidoo EEK, Keasling JD, Beller HR (2012) Engineering of bacterial methyl ketone synthesis for biofuels. Appl Environ Microbiol 78:70–80

    CAS  PubMed  PubMed Central  Google Scholar 

  • Goh E-B, Baidoo EEK, Burd H, Lee TS, Keasling JD, Beller HR (2014) Substantial improvements in methyl ketone production in E. coli and insights on the pathway from in vitro studies. Metab Eng 26:67–76

    CAS  PubMed  Google Scholar 

  • Green EM (2011) Fermentative production of butanol—the industrial perspective. Curr Opin Biotechnol 22:337–343

    CAS  PubMed  Google Scholar 

  • Guo W, Sheng J, Zhao H, Feng X (2016) Metabolic engineering of Saccharomyces cerevisiae to produce 1-hexadecanol from xylose. Microb Cell Fact 15:1–11. https://doi.org/10.1186/s12934-016-0423-9

    Article  CAS  Google Scholar 

  • Ha S, Galazka JM, Rin S, Choi J, Yang X, Seo J (2011) Engineered Saccharomyces cerevisiae capable of simultaneous cellobiose and xylose fermentation. PNAS 108:504–509. https://doi.org/10.1073/pnas.1010456108/-/DCSupplemental.www.pnas.org/cgi/doi/10.1073/pnas.1010456108

    Article  CAS  PubMed  Google Scholar 

  • Hammer SK, Avalos JL (2017) Uncovering the role of branched-chain amino acid transaminases in Saccharomyces cerevisiae isobutanol biosynthesis. Metab Eng 44:302–312. https://doi.org/10.1016/j.ymben.2017.10.001

    Article  CAS  PubMed  Google Scholar 

  • Harrison R, Todd P, Rudge S, Petrides D (2015) Bioprocess design and economics chapter in bioseparations science and engineering. Oxford Press, Oxford. isbn:978-0-19-539181-7

    Google Scholar 

  • Hillson NJ, Hu P, Andersen GL, Shapiro L (2007) Caulobacter crescentus as a whole-cell uranium biosensor. Appl Environ Microbiol 73:7615–7621

    CAS  PubMed  PubMed Central  Google Scholar 

  • Howarth RW (2015) Methane emissions and climatic warming risk from hydraulic fracturing and shale gas development: implications for policy. Energy Emission Control Technol 3:45–45

    Google Scholar 

  • Huang H, Zheng G, Jiang W, Hu H, Lu Y (2015) One-step high-efficiency CRISPR/Cas9-mediated genome editing in Streptomyces. Acta Biochim Biophys Sin 47:231–243

    CAS  PubMed  Google Scholar 

  • Huo Y-X, Cho KM, Rivera JGL, Monte E, Shen CR, Yan Y, Liao JC (2011) Conversion of proteins into biofuels by engineering nitrogen flux. Nat Biotechnol 29(4):346–351. https://doi.org/10.1038/nbt.1789

    Article  CAS  PubMed  Google Scholar 

  • Jagadevan S, Banerjee A, Banerjee C, Guria C, Tiwari R, Baweja M (2018) Recent developments in synthetic biology and metabolic engineering in microalgae towards biofuel production. Biotechnol Biofuels 11:1–21. https://doi.org/10.1186/s13068-018-1181-1

    Article  CAS  Google Scholar 

  • Jang Y-S, Park JM, Choi S, Choi YJ, Seung DY, Cho JH, Lee SY (2012) Engineering of microorganisms for the production of biofuels and perspectives based on systems metabolic engineering approaches. Biotechnol Adv 30(5):989–1000. https://doi.org/10.1016/j.biotechadv.2011.08.0

    Article  CAS  PubMed  Google Scholar 

  • Jansen MLA, Bracher JM, Papapetridis I, Verhoeven MD, de Bruijn H, de Waal PP, van Maris AJA, Klaassen P, Pronk JT (2017) Saccharomyces cerevisiae strains for second-generation ethanol production: from academic exploration to industrial implementation. FEMS Yeast Res 17:fox044

    PubMed Central  Google Scholar 

  • Jeffries TW (2006) Engineering yeasts for xylose metabolism. Curr Opin Biotechnol 17:320–326

    CAS  PubMed  Google Scholar 

  • Jiang Y, Chen B, Duan C, Sun B, Yang J, Yang S (2015) Multigene editing in the Escherichia coli genome via the CRISPR-Cas9 system. Appl Environ Microbiol 81:2506–2514

    CAS  PubMed  PubMed Central  Google Scholar 

  • Jiang YJ, Chen TP, Dong WL, Zhang M, Zhang WM, Wu H, Ma JF, Jiang M, Xin FX (2018) The draft genome sequence of Clostridium beijerinckii NJP7, a unique bacterium capable of producing isopropanol-butanol from hemicellulose through consolidated bioprocessing. Curr Microbiol 75(3):305–308

    CAS  PubMed  Google Scholar 

  • Jiang Y, Wu R, Zhou J, He A, Xu J, Xin F, Zhang W (2019) Recent advances of biofuels and biochemicals production from sustainable resources using co-cultivation systems. Biotechnol Biofuels 12:155. https://doi.org/10.1186/s13068-019-1495-7

    Article  PubMed  PubMed Central  Google Scholar 

  • Jin C, Yao M, Liu H, Lee CFF, Ji J (2011) Progress in the production and application of n-butanol as a biofuel. Renew Sust Energ Rev 15(8):4080–4106

    CAS  Google Scholar 

  • Jones JA, Toparlak ÖD, Koffas MAG (2015) Metabolic pathway balancing and its role in the production of biofuels and chemicals. Curr Opin Biotechnol 33:52–59. https://doi.org/10.1016/j.copbio.2014.11.013

    Article  CAS  PubMed  Google Scholar 

  • Jung H.G and D.A. Deetz (1993). Cell wall lignification and degradability, In: H.G. Jung, D.R. Buxton, R.D. Hatfield, et al. (eds.) Forage cell wall structure and digestibility, ASA-CSSA-SSSA, Madison, pp. 315–346

    Google Scholar 

  • Jung H-JG, Samac DA, Sarath G (2012) Modifying crops to increase cell wall digestibility. Plant Sci 185–186:65–77. https://doi.org/10.1016/j.plantsci.2011.10.014

    Article  CAS  PubMed  Google Scholar 

  • Kalyuzhnaya MG, Puri AW, Lidstrom ME (2015) Metabolic engineering in methanotrophic bacteria. Metab Eng 29:142–152. https://doi.org/10.1016/j.ymben.2015.03.010

    Article  CAS  PubMed  Google Scholar 

  • Kawaguchi H, Hasunuma T, Ogino C, Kondo A (2016) Bioprocessing of bio-based chemicals produced from lignocellulosic feedstocks. Curr Opin Biotechnol 42:30–39. https://doi.org/10.1016/j.copbio.2016.02.031

    Article  CAS  PubMed  Google Scholar 

  • Keeling CI, Bohlmann J (2006) Genes, enzymes, and chemicals of terpenoid diversity in the constitutive and induced defence of conifers against insects and pathogens. New Phytol 170(4):657–675

    CAS  PubMed  Google Scholar 

  • Khalil AS, Collins JJ (2010) Synthetic biology: applications come of age. Nat Publ Group 11(5):367–379. https://doi.org/10.1038/nrg2775

    Article  CAS  Google Scholar 

  • Kim H, Yoo SJ, Kang HA (2015) Yeast synthetic biology for the production of recombinant therapeutic proteins. FEMS Yeast Res 15:1–16. https://doi.org/10.1111/1567-1364.12195

    Article  CAS  PubMed  Google Scholar 

  • Korman TP, Sahachartsiri B, Charbonneau DM, Huang GL, Beauregard M, Bowie JU (2013) Dieselzymes: development of a stable and methanol tolerant lipase for biodiesel production by directed evolution. Biotechnol Biofuels 6:70

    CAS  PubMed  PubMed Central  Google Scholar 

  • Kumar A (2010) Plant genetic transformation and molecular markers. Jaipur, Pointer Publishers, 288 p

    Google Scholar 

  • Kumar A (2013) Biofuels utilisation: an attempt to reduce GHG’s and mitigate climate change. In: Nautiyal S, Rao K, Kaechele H, Raju K, Schaldach R (eds) Knowledge Systems of Societies for adaptation and mitigation of impacts of climate change, Environmental science and engineering. Springer, Berlin, pp 199–224

    Google Scholar 

  • Kumar A (2014) Biotechnology for biofuels: lignocellulosic ethanol production. J Pharm Sci Innov 3(6):495–498. https://doi.org/10.7897/2277-4572.036203

    Article  Google Scholar 

  • Kumar A (2015) Metabolic engineering of plants. In: Bahadur B, VenkatRajam M, Sahijram L, Krishnamurthy KV (eds) Plant biology and biotechnology. Springer, Heidelberg, pp 517–526

    Google Scholar 

  • Kumar A (2020) Synthetic and semi-synthetic metabolic pathways for biofuel production. In: Biofuels: greenhouse gas mitigation and global warming. Springer, New Delhi, pp 421–432

    Google Scholar 

  • Kumar A, Ogita S, Yau YY (eds) (2018) Biofuels: greenhouse gas mitigation and global warming. Next generation biofuels and role of biotechnology. Springer, Heidelberg, 432 p. isbn: 978-81-322-3761-72

    Google Scholar 

  • Kumar A, Bhansali S, Gupta N, Sharma M (2019) Bioenergy and climate change: greenhouse gas mitigation. In: Rastegari AA, Yadav AN, Gupta A (eds) Prospects of renewable bioprocessing in future energy systems, Biofuel and biorefinery technologies, vol 10. Springer, Cham, pp 269–290

    Google Scholar 

  • Kwak S, Jin YS (2017) Production of fuels and chemicals from xylose by engineered Saccharomyces cerevisiae: a review and perspective. Microb Cell Fact 16:1–15. https://doi.org/10.1186/s12934-017-0694-9

    Article  CAS  Google Scholar 

  • Lee SY, Kim HU (2015) Systems strategies for developing industrial microbial strains. Nat Biotechnol 33:1061–1072

    CAS  PubMed  Google Scholar 

  • Lee SK, Chou H, Ham TS, Lee TS, Keasling JD (2008) Metabolic engineering of microorganisms for biofuels production: from bugs to synthetic biology to fuels. Curr Opin Biotechnol 19:556–563. https://doi.org/10.1016/j.copbio.2008.10.014

    Article  CAS  PubMed  Google Scholar 

  • Lee JW et al (2012) Systems metabolic engineering of microorganisms for natural and non-natural chemicals. Nat Chem Biol 8:536–546

    CAS  PubMed  Google Scholar 

  • Leonard E, Kumaran P, Thayer K, Xiao W, Mo JD et al (2010) Combining metabolic and protein engineering of a terpenoid biosynthetic pathway for overproduction and selectivity control. Proc Natl Acad Sci U S A 107:13654–13659. https://doi.org/10.1073/pnas.1006138107/-/DCSupplemental.www.pnas.org/cgi/doi/10.1073/pnas.1006138107

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liao Y-C, Huang T-W, Chen F-C, Charusanti P, Hong JSJ, Chang H-Y, Tsai S-F, Palsson BO, Hsiung CA (2011) An experimentally validated genome-scale metabolic reconstruction of Klebsiella pneumoniae MGH 78578, iYL1228. J Bacteriol 193:1710–1717

    CAS  PubMed  PubMed Central  Google Scholar 

  • Liao JC, Mi L, Pontrelli S, Luo S (2016) Fuelling the future: microbial engineering for the production of sustainable biofuels. Nat Rev Microbiol 14:288–304

    CAS  PubMed  Google Scholar 

  • Lindberg P, Park S, Melis A (2009) Engineering a platform for photosynthetic isoprene production in cyanobacteria, using Synechocystis as the model organism. Metab Eng 12(1):70–79

    PubMed  Google Scholar 

  • Liu W, Yuan JS, Stewart CN Jr (2013) Advanced genetic tools for plant biotechnology. Nat Publ Group 14(11):781–793. https://doi.org/10.1038/nrg3583

    Article  CAS  Google Scholar 

  • Liu J, Li J, Shin H, Liu L, Du G, Chen J (2017) Bioresource technology. Bioresour Technol 239:412–421. https://doi.org/10.1016/j.biortech.2017.04.052

    Article  CAS  PubMed  Google Scholar 

  • Long SP, Marshall-Colon A, Zhu XG (2015) Meeting the global food demand of the future by engineering crop photosynthesis and yield potential. Cell 161:56–66

    CAS  PubMed  Google Scholar 

  • Luterbacher JS, Tester JW, Walker LP (2010) High-solids biphasic CO2-H2O pretreatment of lignocellulosic biomass. Biotechnol Bioeng 107:451–460

    CAS  PubMed  Google Scholar 

  • Lynch MD (2016) Into new territory: improved microbial synthesis through engineering of the essential metabolic network. Curr Opin Biotechnol 38:106–111. https://doi.org/10.1016/j.copbio.2016.01.009

    Article  CAS  PubMed  Google Scholar 

  • Ma T, Shi B, Ye Z, Li X, Liu M, Chen Y, Nielsen J (2019) Lipid engineering combined with systematic metabolic engineering of Saccharomyces cerevisiae for high-yield production of lycopene. Metab Eng 52:134–142. https://doi.org/10.1016/j.ymben.2018.11.009

    Article  CAS  PubMed  Google Scholar 

  • Mackenzie A (2013) Synthetic biology and the technicity of biofuels. Stud Hist Philos Biol Biomed Sci 44(2):190–198. https://doi.org/10.1016/j.shpsc.2013.03.014

    Article  PubMed  Google Scholar 

  • Marella ER, Holkenbrink C, Siewers V, Borodina I (2018) Engineering microbial fatty acid metabolism for biofuels and biochemicals. Curr Opin Biotechnol 50:39–46. https://doi.org/10.1016/j.copbio.2017.10.002

    Article  CAS  PubMed  Google Scholar 

  • Martien JI, Amador-Noguez D (2017) Recent applications of metabolomics to advance microbial biofuel production. Curr Opin Biotechnol 43:118–126. https://doi.org/10.1016/j.copbio.2016.11.006

    Article  CAS  PubMed  Google Scholar 

  • Martín del Campo JS, Rollin J, Myung S, Chun Y, Chandrayan S, Patiño R et al (2013) High-yield production of dihydrogen from xylose by using a synthetic enzyme cascade in a cell-free system. Angew Chem Int Ed 52(17):4587–4590

    Google Scholar 

  • Mcanulty MJ, Poosarla VG, Li J, Soo VWC, Zhu F, Wood TK (2017) Metabolic engineering of Methanosarcina acetivorans for lactate production from methane. Biotechnol Bioeng 114:852–861. https://doi.org/10.1002/bit.26208

    Article  CAS  PubMed  Google Scholar 

  • Meyer MT, McCormick AJ, Griffiths H (2016) Will an algal CO2-concentrating mechanism work in higher plants? Curr Opin Plant Biol 31:181–188

    CAS  PubMed  Google Scholar 

  • Myung S, Rollin J, You C, Sun F, Chandrayan S, Adams MWW et al (2014) In vitro metabolic engineering of hydrogen production at theoretical yield from sucrose. Metab Eng 24(1):70–77

    CAS  PubMed  Google Scholar 

  • Nielsen J, Keasling JD (2011) Synergies between synthetic biology and metabolic engineering. Nat Biotechnol 29:693–695

    CAS  PubMed  Google Scholar 

  • Nielsen J, Keasling JD (2016) Engineering cellular metabolism. Cell 164(6):1185–1197. https://doi.org/10.1016/j.cell.2016.02.004

    Article  CAS  PubMed  Google Scholar 

  • O’Connor SE (2015) Engineering of secondary metabolism. Annu Rev Genet 49:71–94

    PubMed  Google Scholar 

  • Oh JH, van Pijkeren JP (2014) CRISPR-Cas9-assisted recombineering in Lactobacillus reuteri. Nucleic Acids Res 42:e131

    PubMed  PubMed Central  Google Scholar 

  • Peralta-Yahya PP, Keasling JD (2010) Advanced biofuel production in microbes. Biotechnol J 5:147–162

    CAS  PubMed  Google Scholar 

  • Peralta-Yahya PP, Ouellet M, Chan R, Mukhopadhyay A, Keasling JD, Lee TS (2011) Identification and microbial production of a terpene-based advanced biofuel. Nat Commun 2:483–488. https://doi.org/10.1038/ncomms1494

    Article  CAS  PubMed  Google Scholar 

  • Peralta-Yahya PP et al (2012) Microbial engineering for the production of advanced biofuels. Nature 488:320–328. https://doi.org/10.1038/nature488320-328

    Article  CAS  PubMed  Google Scholar 

  • Raschmanová H, Weninger A, Glieder A, Kovar K, Vogl T (2018) Implementing CRISPR-Cas technologies in conventional and non- conventional yeasts: current state and future prospects. Biotechnol Adv 36(3):641–665. https://doi.org/10.1016/j.biotechadv.2018.01.006

    Article  CAS  PubMed  Google Scholar 

  • Renniger N, McPhee D (2008) Fuel compositions comprising farnesane and farnesane derivatives and method of making and using same. US Patent No. 7399323

    Google Scholar 

  • Rogelj J, Hare W, Lowe J, van Vuuren DP, Riahi K, Matthews B, Meinshausen M et al (2011) Emission pathways consistent with a 2°C global temperature limit. Nat Clim Chang 1(8):413–418. https://doi.org/10.1038/nclimate1258

    Article  Google Scholar 

  • Rollin JA, Ye XH, Del Campo JM, Adams MWW, Zhang Y-HP (2016) Novel hydrogen detection apparatus along with bioreactor systems. Adv Biochem Eng Biotechnol 152:35–51. https://doi.org/10.1007/10_2014_274

    Article  CAS  PubMed  Google Scholar 

  • Salazar M, Vongsangnak W, Panagiotou G, Andersen MR, Nielsen J (2009) Uncovering transcriptional regulation of glycerol metabolism in Aspergilli through genome-wide gene expression data analysis. Mol Gen Genomics 282:571–586

    CAS  Google Scholar 

  • Sanford K, Chotani G, Danielson N, Zahn JA (2016) Scaling up of renewable chemicals. Curr Opin Biotechnol 38:112–122. https://doi.org/10.1016/j.copbio.2016.01.008

    Article  CAS  PubMed  Google Scholar 

  • Santos F, Boele J, Teusink B (2011) A practical guide to genome-scale metabolic models and their analysis. Methods Enzymol 500:509–532

    CAS  PubMed  Google Scholar 

  • Savakis P, Hellingwerf KJ (2015) Engineering cyanobacteria for direct biofuel production from CO2. Curr Opin Biotechnol 33:8–14

    CAS  PubMed  Google Scholar 

  • Scheffers BR, De Meester L, Bridge TC, Hoffmann AA, Pandolfi JM, Corlett RT, Butchart SH, Pearce-Kelly P, Kovacs KM, Dudgeon D et al (2016) The broad footprint of climate change from genes to biomes to people. Science 354(6313):719

    CAS  Google Scholar 

  • Shaik N, Kumar A (2014) Energy crops for biofuel and food security. J Pharm Sci Innov 3:507–515

    Google Scholar 

  • Shanmugam S, Sun C, Zeng X, Wu YR (2018) High-efficient production of biobutanol by a novel Clostridium sp. strain WST with uncontrolled pH strategy. Bioresour Technol 256:543–547

    CAS  PubMed  Google Scholar 

  • Shih PM, Zarzycki J, Niyogi KK, Kerfeld CA (2014) Introduction of a synthetic CO2-fixing photorespiratory bypass into a cyanobacterium. J Biol Chem 289:9493–9500

    CAS  PubMed  PubMed Central  Google Scholar 

  • Shindell D, Kuylenstierna JCI, Vignati E, Dingenen R, Amann M, Klimont Z, Anenberg S, Muller N, Janssens-Maenhout G, Raes F, Schwartz J, Faluvegi G, Pozzoli L, Kupiainen K, Höglund-Isaksson L, Emberson L, Streets D, Ramanathan V, Hicks K, Oanh NT, Milly G, Williams M, Demkine V, Fowler D (2012) Simultaneously mitigating near-term climate change and improving human health and food security. Science 335:183–189

    CAS  PubMed  Google Scholar 

  • Sitepu IR, Garay LA, Sestric R, Levin D, Block DE, Bruce GJ, Boundy-Mills KL (2014) Oleaginous yeasts for biodiesel: current and future trends in biology and production. Biotechnol Adv 32(7):1336–1360. https://doi.org/10.1016/j.biotechadv.2014.08.003

    Article  CAS  PubMed  Google Scholar 

  • Soo VW, McAnulty MJ, Tripathi A, Zhu F, Zhang L, Hatzakis E, Smith PB, Agrawal S, Nazem-Bokaee H, Gopalakrishnan S, Salis HM, Ferry JG, Maranas CD, Patterson AD, Wood TK (2016) Reversing methanogenesis to capture methane for liquid biofuel precursors. Microb Cell Fact 15:11

    PubMed  PubMed Central  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • Sun C, Zhang S, Xin FX, Shanmugam S, Wu YR (2018) Genomic comparison of Clostridium species with the potential of utilizing red algal biomass for biobutanol production. Biotechnol Biofuels 11:42

    PubMed  PubMed Central  Google Scholar 

  • Swartz JR (2013) Cell-free bioprocessing. Chem Eng Prog 11:40–45

    Google Scholar 

  • Taheripour TMF, Zhuang Q, Tyner WE, Lu X (2012) Biofuels, cropland expansion, and the extensive margin. Energy Sustain Soc 2:25

    Google Scholar 

  • Tatsis EC, O’Connor SE (2016) New developments in engineering plant metabolic pathways. Curr Opin Biotechnol 42:126–132. https://doi.org/10.1016/j.copbio.2016.04.012

    Article  CAS  PubMed  Google Scholar 

  • Thauer RK, Kaster AK, Seedorf H, Buckel W, Hedderich R (2008) Methanogenic archaea: ecologically relevant differences in energy conservation. Nat Rev Microbiol 6:579–591

    CAS  PubMed  Google Scholar 

  • Tholl D (2006) Terpene synthases and the regulation, diversity and biological roles of terpene metabolism. Curr Opin Plant Biol 9(3):297–304

    CAS  PubMed  Google Scholar 

  • Tong Y, Charusanti P, Zhang L, Weber T, Lee SY (2015) CRISPR-Cas9 based engineering of actinomycetal genomes. ACS Synth Biol 4:1020–1029

    CAS  PubMed  Google Scholar 

  • Tran P, Hoang N, Ko JK, Gong G, Um Y, Lee SM (2018) Biotechnology for biofuels genomic and phenotypic characterization of a refactored xylose-utilizing Saccharomyces cerevisiae strain for lignocellulosic biofuel production. Biotechnol Biofuels 11:1–13. https://doi.org/10.1186/s13068-018-1269-7

    Article  CAS  Google Scholar 

  • Trindade WRDS, Santos RGD (2017) Review on the characteristics of butanol, its production and use as fuel in internal combustion engines. Renew Sust Energ Rev 69:642–651

    Google Scholar 

  • Tyner WE (2012) Biofuels and agriculture: a past perspective and uncertain future. Int J Sustain Dev World Ecol 19:389–394

    Google Scholar 

  • Tyo KE, Ajikumar PK, Stephanopoulos G (2009) Stabilized gene duplication enables long- term selection-free heterologous pathway expression. Nat Biotechnol 27(8):760–765

    CAS  PubMed  Google Scholar 

  • US DOE (2010) National algal biofuels technology roadmap. United States Department of Energy

    Google Scholar 

  • US Energy Information Administration (2012). http://www.eia.gov. (US Energy Information Administration)

  • Van Vleet JH, Jeffries TW (2009) Yeast metabolic engineering for hemicellulosic ethanol production. Curr Opin Biotechnol 20:300–306

    PubMed  Google Scholar 

  • Völler J-S, Budisa N (2017) Coupling genetic code expansion and metabolic engineering for synthetic cells. Curr Opin Biotechnol 48:1–7. https://doi.org/10.1016/j.copbio.2017.02.002

    Article  CAS  PubMed  Google Scholar 

  • Wang W, Sun J, Hartlep M, Deckwer W-D, Zeng A-P (2003) Combined use of proteomic analysis and enzyme activity assays for metabolic pathway analysis of glycerol fermentation by Klebsiella pneumoniae. Biotechnol Bioeng 83:525–536

    CAS  PubMed  Google Scholar 

  • Wang J, Guleria S, Koffas MA, Yan Y (2015) Microbial production of value-added nutraceuticals. Curr Opin Biotechnol 37:97–104

    PubMed  Google Scholar 

  • Wang C, Pfleger BF, Kim S (2017) Reassessing Escherichia coli as a cell factory for biofuel production. Curr Opin Biotechnol 45:92–103. https://doi.org/10.1016/j.copbio.2017.02.010

    Article  CAS  PubMed  Google Scholar 

  • Wess J, Brinek M, Boles E (2019) Improving isobutanol production with the yeast Saccharomyces cerevisiae by successively blocking competing metabolic pathways as well as ethanol and glycerol formation. Biotechnol Biofuels 12:173. https://doi.org/10.1186/s13068-019-1486-8

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wohlbach DJ, Kuo A, Sato TK, Potts KM, Salamov AA, Labutti KM, Sun H (2011) Comparative genomics of xylose-fermenting fungi for enhanced biofuel production. PNAS 108:13213. https://doi.org/10.1073/pnas.1103039108/-/DCSupplemental.www.pnas.org/cgi/doi/10.1073/pnas.1103039108

    Article  Google Scholar 

  • Woo HM (2017) Solar-to-chemical and solar-to-fuel production from CO2 by metabolically engineered microorganisms. Curr Opin Biotechnol 45:1–7. https://doi.org/10.1016/j.copbio.2016.11.017

    Article  CAS  PubMed  Google Scholar 

  • Woodward J, Orr M, Cordray K, Greenbaum E (2000) Enzymatic production of biohydrogen. Nature 405:1014–1015

    CAS  PubMed  Google Scholar 

  • Wu J et al (2015) Enhancing flavonoid production by systematically tuning the central metabolic pathways based on a CRISPR interference system in Escherichia coli. Sci Rep 5:13477

    PubMed  PubMed Central  Google Scholar 

  • Yao L et al (2016) Multiple gene repression in cyanobacteria using CRISPRi. ACS Synth Biol 5:207–212

    CAS  PubMed  Google Scholar 

  • Ye X, Wang Y, Hopkins RC, Adams MWW, Evans BR, Mielenz JR et al (2009) Spontaneous high- yield production of hydrogen from cellulosic materials and water catalyzed by enzyme cocktails. ChemSusChem 2(2):149–152

    CAS  PubMed  Google Scholar 

  • Yu L, Xu M, Tang I-C, Yang S-T (2015) Metabolic engineering of\n Clostridium tyrobutyricum\n for n-butanol production through co-utilization of glucose and xylose. Biotechnol Bioeng 112(10):2134–2141. https://doi.org/10.1002/bit.25613

    Article  CAS  PubMed  Google Scholar 

  • Zhang Y-HP (2011) Simpler is better: high-yield and potential low-cost biofuels production through cell-free synthetic pathway biotransformation (SyPaB). ACS Catal 1:998–1009

    CAS  Google Scholar 

  • Zhang Y-HP (2015) Production of biofuels and biochemicals by in vitro synthetic biosystems: opportunities and challenges. Biotechnol Adv 33(7):1467–1483. https://doi.org/10.1016/j.biotechadv.2014.10.009

    Article  CAS  PubMed  Google Scholar 

  • Zhang Y-HP, Evans BR, Mielenz JR, Hopkins RC, Adams MWW (2007) High-yield hydrogen production from starch and water by a synthetic enzymatic pathway. PLoS One 2(5):e456

    PubMed  PubMed Central  Google Scholar 

  • Zheng T, Olson DG, Tian L, Bomble YJ, Himmel ME, Lo J, Hon S, Shaw AJ, van Dijken JP, Lynd LR (2015) Cofactor specificity of the bifunctional alcohol and aldehyde dehydrogenase (AdhE) in wild-type and mutant Clostridium thermocellum and Thermoanaerobacterium saccharolyticum. J Bacteriol 197(15):2610–2619

    CAS  PubMed  PubMed Central  Google Scholar 

  • Zhu Q, Jackson EN (2015) Metabolic engineering of Yarrowia lipolytica for industrial applications. Curr Opin Biotechnol 36:65–72. https://doi.org/10.1016/j.copbio.2015.08.010

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

The author acknowledges support from Alexander von Humboldt Foundation (Germany) to work in the laboratory of Late Professor Dr. K-H. Neumann and later on Professor Dr. Sven Schubert at the Institut für Pflanzenernährung, Justus Liebig University, Gießen, Germany, and the Japanese Society for Promotion of Science (JSPS) fellowship to work with Professor Shinjiro Ogita during the course of investigations spreading over 20 years. Financial support from the Department of Biotechnology, Govt. of India, New Delhi, and infrastructural support for providing 50 ha land area for experimentation by the University of Rajasthan Syndicate are gratefully acknowledged. I also acknowledge my research scholars and technical staff who have worked in the lab and field with me for investigations presented here. I also thank my wife Professor Vijay R. Kumar for going through the manuscript and making suggestions.

I also acknowledge with thanks the different figures with legends reproduced with permissions from the following publications: Figure 11.1. Alper, H. & Stephanopoulos, G. (2009). Engineering for biofuels: exploiting innate microbial capacity or importing biosynthetic potential, Nature Reviews. Microbiology 7: 715–723. Retrieved from https://doi.org/10.1038/nrmicro2186. Reproduced with license number 46456408400514. Figure 11.2. Liao, J. C., Mi, L., Pontrelli, S. & Luo, S. (2016). Fuelling the future: microbial engineering for the production of sustainable biofuels. Nature Publishing Group, Nature Review. Microbiology 14(5): 288–304. https://doi.org/10.1038/nrmicro.2016.32. Reproduced under license number 4645730007098. Figure 11.3. Martien J.I. and Amador-Noguez D. (2017). Recent applications of metabolomics to advance microbial biofuel production. Current Opinion in Biotechnology, 43, 118–126. https://doi.org/10.1016/j.copbio.2016.11.006. Reproduced with permission license number 4666750205840. Figure 11.4. Jones, J.A., Toparlak, Duhan, Ö., and Koffas, Mattheos AG (2015). Metabolic pathway balancing and its role in the production of biofuels and chemicals. Current Opinion in Biotechnology 33, 52–59. https://doi.org/10.1016/j.copbio.2014.11.013. Reproduced with permission no 4671031226483. Figures 11.5 and 11.6. Peralta-Yahya, P. P., Ouellet, M., Chan, R., Mukhopadhyay, A., Keasling, J. D., & Lee, T. S. (2011). Identification and microbial production of a terpene-based advanced biofuel. Nature Communications 2(May): 483–488. https://doi.org/10.1038/ncomms1494. This is an open-access article distributed under the terms of the Creative Commons CC-BY license, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Figures 11.7 and 11.8. Ma, T., Shi, B., Ye, Z., Li, X., Liu, M., Chen, Y. & Nielsen, J. (2019). Lipid engineering combined with systematic metabolic engineering of Saccharomyces cerevisiae for high-yield production of lycopene. Metabolic Engineering 52(November 2018): 134–142. https://doi.org/10.1016/j.ymben.2018.11.009. Reproduced under license number 4651230668162. Figure 11.9. Peralta-Yahya P. P. et al. (2012). Microbial engineering for the production of advanced biofuels. https://doi.org/10.1038/nature488320–328. Reproduced with license no. 4643340791481. Figure 11.10. Zhang, Y. P. (2015). Production of biofuels and biochemicals by in vitro synthetic biosystems: Opportunities and challenges. Biotechnology Advances 33(7): 1467–1483. https://doi.org/10.1016/j.biotechadv.2014.10.009. Reproduced with license number 4652950482642. Figure 11.11. Jagadevan, S., Banerjee, A., Banerjee, C., Guria, C., Tiwari, R., & Baweja, M. (2018). Biotechnology for Biofuels Recent developments in synthetic biology and metabolic engineering in microalgae towards biofuel production. Biotechnology for Biofuels 11: 1–21. https://doi.org/10.1186/s13068-018-1181-1. Used under creative commons license. Figures 11.12, 11.13, and 11.14. Georgianna, D. R. & Stephen, P. (2012). Exploiting diversity and synthetic biology for the production of algal biofuels. Nature 488: 330-335. https://doi.org/10.1038/nature11479. Reproduced under license number 4646381493445. Figure 11.15. Huo, Y.-X., Cho, K. M., Rivera, J. G. L., Monte, E., Shen, C. R., Yan, Y. & Liao, J. C. (2011). Conversion of proteins into biofuels by engineering nitrogen flux. Nature Biotechnology 29(4): 346–351. https://doi.org/10.1038/nbt.1789. Reproduced with permission under license number 4646190098001 from RightsLink.

Author information

Authors and Affiliations

  1. Department of Botany, University of Rajasthan, Jaipur, India

    Ashwani Kumar

Authors
  1. Ashwani Kumar
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Department of Botany and P.G. School of Biotechnology, University of Rajasthan, Jaipur, Rajasthan, India

    Ashwani Kumar

  2. Department of Natural Sciences, Northeastern State University, Broken Arrow, OK, USA

    Yuan-Yeu Yau

  3. Faculty of Life and Environmental Sciences, Department of Life Sciences, Prefectural University of Hiroshima, Syoubara, Hiroshima, Japan

    Shinjiro Ogita

  4. Faculty of Biology and Chemistry, Plant Physiology, University of Osnabrück, Osnabrück, Niedersachsen, Germany

    Renate Scheibe

Rights and permissions

Reprints and permissions

Copyright information

© 2020 Springer Nature Singapore Pte Ltd.

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Kumar, A. (2020). Synthetic Biology and Future Production of Biofuels and High–Value Products. In: Kumar, A., Yau, YY., Ogita, S., Scheibe, R. (eds) Climate Change, Photosynthesis and Advanced Biofuels. Springer, Singapore. https://doi.org/10.1007/978-981-15-5228-1_11

Download citation

Publish with us

Policies and ethics

Search

Navigation