Skip to main content
SpringerLink
Log in

Metabolic Engineering and Synthetic and Semi-Synthetic Pathways: Biofuel Production for Climate Change Mitigation

  • Chapter
  • First Online:
Biotechnological Innovations for Environmental Bioremediation

  • 991 Accesses

Abstract

The Green Revolution has fueled an exponential growth in human population since the mid- twentieth century. Due to population growth, food and energy demands will soon surpass supply capabilities. Plant genetic engineering has the potential to overcome some of these challenges. As an example, bioenergy crops can be genetically improved for producing more biomass, being more resilient to stresses like drought conditions and pathogens. Besides they can synthesize cell wall materials with reduced recalcitrance toward deconstruction processes. This strategy has been put forward for the environmentally sustainable production of fuels and chemicals currently derived from petroleum refining. Industrial crops produce feedstocks for fabricating fiber, biopolymer, and construction materials. These crops offer the potential to reduce our dependency on petrochemicals that currently serve as building blocks for manufacturing the majority of our industrial and consumer products. 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 a 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 219.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 279.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 279.99
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

Similar content being viewed by others

References

  • Anosova I, Kowal EA, Dunn MR, Chaput JC, Van Horn WD, Egli M (2015) The structural diversity of artificial genetic polymers. Nucl Acids Res 44(3):1007–1021. https://doi.org/10.1093/nar/gkv1472

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ashour M, Wink M, Gershenzon J (2010) Biochemistry of terpenoids: monoterpenes, sesquiterpenes and diterpenes. In: Wink M (ed), Annual plant reviews. Biochemistry of plant secondary metabolism, vol 40, pp 258–303

    Google Scholar 

  • Ausländer S, Ausländer D, Fussenegger M (2017) Synthetic biology—the synthesis of biology. Angew Chem Int Ed 56:6396

    Article  CAS  Google Scholar 

  • Bailey-Serres J, Parker JE, Ainsworth EA, Oldroyd GED, Schroeder JI (2019) Genetic strategies for improving crop yields. Nature 575:109–111

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Banerjee A, Sharkey TD (2014) Methylerythritol 4-phosphate (MEP) pathway metabolic regulation. Nat Prod Rep 31:1043–1055

    Article  CAS  PubMed  Google Scholar 

  • Barbacka K, Baer-Dubowska W (2011) Searching for artemisinin production improvement in plants and microorganisms. Curr Pharm Biotechnol 12:1743–1751

    Article  CAS  PubMed  Google Scholar 

  • Bartley BA, Kim K, Medley JK, Sauro HM (2017) Synthetic biology: engineering living systems from biophysical principles. Biophys J 112(6):1050–1058. https://doi.org/10.1016/j.bpj.2017.02.013

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Baxter HL, Mazarei M, Fu C et al (2016) Time course field analysis of COMT-downregulated switchgrass: lignification, recalcitrance, and rust susceptibility. Bioenergy Res 9:1087–1100

    Article  CAS  Google Scholar 

  • Baxter HL, Mazarei M, Labbe N, Kline LM, Cheng Q, Windham MT, Mann DGJ, Chunxiang F, Ziebell A, Sykes RW, Rodriguez M Jr, Davis MF, Mielenz JR, Dixon RA, Wang Z-Y, Stewart CN Jr (2014) Two-year field analysis of reduced recalcitrance transgenic switchgrass. Plant Biotechnol J 12(7):914–924

    Article  PubMed  Google Scholar 

  • Beekwilder J, Wolswinkel R, Jonker H, Hall R, de Vos CH, Bovy A (2006) Production of resveratrol in recombinant microorganisms. Appl Environ Microbiol 72:5670–5672

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bender L, Kumar A, Neumann KH (1985) On the photosynthetic system and assimilate metabolism of daucus and arachis cell cultures. In: Neumann KH, Barz W, Reinhard E (eds) Primary and secondary metabolism of plant cell cultures. Proceedings in life sciences. Springer, Berlin. https://doi.org/10.1007/978-3-642-70717-9_3

    Chapter  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 

  • Brophy JA, Voigt CA (2014) Principles of genetic circuit design. Nat Methods 11(5):508–520. https://doi.org/10.1038/nmeth.2926

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Byrt CS, Grof CP, Furbank RT (2011) C4 plants as biofuel feedstocks: optimising biomass production and feedstock quality from a lignocellulosic perspective. J Integr Plant Biol 53(2):120–135. https://doi.org/10.1111/j.1744-7909.2010.01023.x

    Article  CAS  PubMed  Google Scholar 

  • Cameron DE, Bashor CJ, Collins JJ (2014a) A brief history of synthetic biology. Nat Rev Microbiol 12:381–390

    Article  CAS  PubMed  Google Scholar 

  • Cameron DE, Bashor CJ, Collins JJA (2014b) Brief history of synthetic biology. Nat Rev Microbiol 12:381–390

    Article  CAS  PubMed  Google Scholar 

  • Carroll D (2011) Genome engineering with zinc-finger nucleases. Genetics 188:773–782

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chanoca A, de Vries L, Boerjan W (2019) Lignin engineering in forest trees. Front Plant Sci 10:912. https://doi.org/10.3389/fpls.2019.00912

    Article  PubMed  PubMed Central  Google Scholar 

  • Chao R, Yuan Y, Zhao H (2015) Recent advances in DNA assembly technologies. FEMS Yeast Res 15(1):1–9. https://doi.org/10.1111/1567-1364.12171

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Christianson DW (2017) Structural and chemical biology of terpenoid cyclases. Chem Rev 117:11570–11648

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Christian M, Cermak T, Doyle EL, Schmidt C, Zhang F et al (2010) Targeting DNA double-strand breaks with TAL effector nucleases. Genetics 186:757–761

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Christin P-A, Osborne CP (2013) The recurrent assembly of C4 photosynthesis, an evolutionary tale. Photosynth Res 117(1–3):163–175

    Article  CAS  PubMed  Google Scholar 

  • Chun-Fu WU, Yang JY, Wang F, Wang XX (2013) Resveratrol: botanical origin, pharmacological activity and applications. Chin J Nat Med 11:1–15

    Google Scholar 

  • Cordoba E, Salmi M, León P (2009) Unravelling the regulatory mechanisms that modulate the MEP pathway in higher plants. J Exp Bot 60:2933–2943

    Article  CAS  PubMed  Google Scholar 

  • DeLisi C (2019) The role of synthetic biology in climate change mitigation. Biol Direct 14:14. https://doi.org/10.1186/s13062-019-0247-8

    Article  PubMed  PubMed Central  Google Scholar 

  • Deltcheva E, Chylinski K, Sharma CM, Gonzales K, Chao Y, Pirzada ZA, Eckert MR, Vogel J, Charpentier E (2011) CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. Nature 471:602. https://doi.org/10.1038/nature09886

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • DiMario RJ, Quebedeaux JC, Longstreth DJ, Dassanayake M, Hartman MM, Moroney JV (2016) The cytoplasmic carbonic anhydrases βCA2 and βCA4 are required for optimal plant growth at low CO2. Plant Physiol 171:280–293

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Endler A, Persson S (2011) Cellulose synthases and synthesis in Arabidopsis. Mol Plant 4:199–211

    Article  CAS  PubMed  Google Scholar 

  • Ermakova M, Danila FR, Furbank RT, von Caemmerer S (2020) On the road to C4 rice: advances and perspectives. Plant J 101:940–950

    Article  CAS  PubMed  Google Scholar 

  • di Fagagna FDA (2014) A direct role for small non-coding RNAs in DNA damage response. Trends Cell Biol 24:171–178. https://doi.org/10.1016/j.tcb.2013.09.008

    Article  CAS  Google Scholar 

  • Fu C, Mielenz JR, Xiao X, Ge Y, Hamilton CY, Rodriguez M Jr, Chen F, Foston M, Ragauskas A, Bouton J, Dixon RA, Wang Z-Y (2011) Genetic manipulation of lignin reduces recalcitrance and improves ethanol production from switchgrass. Proc Natl Acad Sci U S A 108(9):3803–3808. https://doi.org/10.1073/pnas.1100310108

    Article  PubMed  PubMed Central  Google Scholar 

  • Fuentes P, Zhou F, Erban A, Karcher D, Kopka J, Bock R (2016) A new synthetic biology approach allows transfer of an entire metabolic pathway from a medicinal plant to a biomass crop. elife 5:e13664

    Article  PubMed  PubMed Central  Google Scholar 

  • Gajraj Randhir S, Singh GP, Kumar A (2018) Third-generation biofuel: algal biofuels as a sustainable energy source. 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 307–326

    Google Scholar 

  • Gerland P, Raftery AE, Sevcikova H, Li N, Gu D, Spoorenberg T, Alkema L, Fosdick BK, Chunn J, Lalic N, Bay G, Buettner T, Heilig GK, Wilmoth J (2014) World population stabilization unlikely this century. Science 346:234–237

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Handakumbura PP, Hazen SP (2012) Transcriptional regulation of grass secondary cell wall biosynthesis: playing catch-up with Arabidopsis thaliana. Front Plant Sci 3:74

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hemmerlin A, Harwood JL, Bach TJ (2012) A raison d‘être for two distinct pathways in the early steps of plant isoprenoid biosynthesis? Prog Lipid Res 51:95–148

    Article  CAS  PubMed  Google Scholar 

  • Hibberd JM, Covshoff S (2010) The regulation of gene expression required for C4 photosynthesis. Annu Rev Plant Biol 61:181–207

    Article  CAS  PubMed  Google Scholar 

  • Hirani AH, Javed N, Asif M, Basu SK, and Kumar A (2018) A review on first- and second-generation biofuel productions Kumar A, Ogita S, Yau Y-Y Biofuels: greenhouse gas mitigation and global warming next generation biofuels and role of biotechnology, Springer Heidelberg141–154

    Google Scholar 

  • Hugh DG, Wright P, Hailstones D (2018) Emerging opportunities for synthetic biology in agriculture. Genes 9:341–357. Return to ref 9 in article

    Article  CAS  Google Scholar 

  • Jez J, Soon GL, Sherp A (2016) The next green movement: plant biology for the environment and sustainability. Science 353:1241–1244

    Article  CAS  PubMed  Google Scholar 

  • Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E (2012) A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337:816–821. https://doi.org/10.1126/science.1225829

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kalluri UC, Yin H, Yang X, Davison BH (2014) Systems and synthetic biology approaches to alter plant cell walls and reduce biomass recalcitrance. Plant Biotechnol J:1207–1216. https://doi.org/10.1111/pbi.12283

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kumar A (2015) Metabolic engineering in plants. In: Bahadur B, Rajam MV, Sahijram L, Krishnamurthy KV (eds) Plant biology and biotechnology. II Plant genomics and biotechnology. Springer, New Delhi, pp 517–526

    Chapter  Google Scholar 

  • Kumar A (2018a) Alternative biomass from semiarid and arid conditions as a biofuel source: Calotropis procera and its genomic characterization. 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 241–270

    Google Scholar 

  • Kumar A (2018b) Global warming, climate change and greenhouse gas mitigation. 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 1–16

    Google Scholar 

  • Kumar A, Ogita S, Yau Y-Y (eds) (2018c) Biofuels: greenhouse gas mitigation and global warming next generation biofuels and role of biotechnology. Springer, Heidelberg, pp 432

    Google Scholar 

  • Kumar A, Yau YY, Ogita S, Scheibe R (eds) (2020) Climate change, photosynthesis and advanced biofuels. Springer, Singapore, pp 490. https://doi.org/10.1007/978-981-15-5228-1_1

  • 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, pp 271–302. https://doi.org/10.1007/978-981-15-5228-1_11

    Chapter  Google Scholar 

  • Kumar A, Bender L, Neumann KH (1984) Growth regulation plastid differentiation and the development of photosynthetic system in cultured carrot root explants as influenced by exogenous sucrose and various phytohormones. Plant Cell Tissue Organ Cult 3:11–28

    Article  CAS  Google Scholar 

  • Kumar A, Bender L, Pauler B, Neumann K-H, Senger H, Jeske C (1983) Ultrastructural and biochemical development of the photosynthetic apparatus during callus induction in carrot root explants. Plant Cell Tissue Organ Cult 2:161–177

    Article  CAS  Google Scholar 

  • Kumar A, Gupta N (2018) Potential of lignocellulosic materials for production of ethanol. 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 271–290

    Google Scholar 

  • Kumar S, Hahn FM, Baidoo E, Kahlon TS, Wood DF, McMahan CM, Whalen MC (2012) Remodeling the isoprenoid pathway in tobacco by expressing the cytoplasmic mevalonate pathway in chloroplasts. Metab Eng 14:19–28

    Article  CAS  PubMed  Google Scholar 

  • Kumar A, Sharma M, Basu SK, Asif M, Li XP, Chen X (2014) Plant molecular breeding: perspectives from the plant biotechnology and market assisted selection. In: Benkeblia N (ed) Omics technologies and crops improvement. CRC Press, Boca Raton, FL, pp 153–168

    Google Scholar 

  • Kumar A, Abraham E, Arti G (2018a) Alternative biomass from saline and semiarid and arid conditions as a source of biofuels: Salicornia. 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 229–240

    Google Scholar 

  • Kumar AS, Bhansali N, Gupta SM (2018b) Bioenergy and climate change: greenhouse gas mitigation. In: Yadav AN et al (eds) Prospects of renewable bioprocessing in future energy systems. Springer, Heidelberg

    Google Scholar 

  • Kumar A, Khandelwal SG, Gadhwal N (2022a) Global environmental problems: a nexus between climate , human health and COVID 19 and evolving mitigation strategies. In: Sudipti A, Kumar A, Ogita S, Yau YY (eds) Innovations in environment biotechnology. Springer, Cham, pp 67–112

    Google Scholar 

  • Kumar A, Acharya P, Jaiman V (2022b) Third generation hybrid technology for algal biomass production, wastewater treatment and greenhouse gas mitigation. In: Sudipti A, Kumar A, Ogita S, Yau YY (eds) Innovations in environment biotechnology. Springer, Cham, pp 229–266

    Google Scholar 

  • Kumar A, Witharana C, Arora S, Saxena S, Yau Y-Y (2022c) Metabolic engineering and synthetic and semi-synthetic pathways: biofuel production for climate change mitigation. In: Arora S, Kumar A, Ogita S, Yau YY (eds) Biotechnological innovations for bioremediation. Springer, Cham

    Google Scholar 

  • Kumar A, Rani A, Choudhary M (2022d) Anaerobic digestion for climate change mitigation: a review. In: Arora S, Kumar A, Ogita S, Yau YY (eds) Biotechnological innovations for bioremediation. Springer, Cham

    Google Scholar 

  • Kumawat S, Rana N, Bansal R, Vishwakarma G, Mehetre S, Das BK (2019) Fast neutron mutagenesis in plants: advances, applicability and challenges. Plants 8:164

    Article  CAS  PubMed Central  Google Scholar 

  • Kumlehn J, Pietralla J, Hensel G, Pacher M, Puchta H (2018) The CRISPR/Cas revolution continues: from efficient gene editing for crop breeding to plant synthetic biology. J Integr Plant Biol 60:1127–1153

    Article  CAS  PubMed  Google Scholar 

  • Lee J-H, Wendisch VF (2017) Biotechnological production of aromatic compounds of the extended shikimate pathway from renewable biomass. J Biotechnol 257:211–221

    Article  CAS  PubMed  Google Scholar 

  • Li X, Weng JK, Chapple C (2008) Improvement of biomass through lignin modification. Plant J 54:569–581

    Article  CAS  PubMed  Google Scholar 

  • Li M, Hou F, Wu T, Jiang X, Li F, Liu H, Xian M, Zhang H (2020) Recent advances of metabolic engineering strategies in natural isoprenoid production using cell factories. Nat Prod Rep 37:80–99. https://doi.org/10.1039/C9NP00016J

    Article  CAS  PubMed  Google Scholar 

  • Liang Y, Richardson S, Yan J, Benites VT, Cheng-Yue C, Tran T, Mortimer J, Mukhopadhyay A, Keasling JD, Scheller HV, Loque D (2017) Endoribonuclease-based two- component repressor systems for tight gene expression control in plants. ACS Synth Biol 6:806–816

    Article  CAS  PubMed  Google Scholar 

  • Lin CY, Eudes A (2020) Strategies for the production of biochemicals in bioenergy crops. Biotechnol Biofuels 13:71. https://doi.org/10.1186/s13068-020-01707-x

    Article  PubMed  PubMed Central  Google Scholar 

  • Liu W, Stewart CN Jr (2015) Plant synthetic biology. Trends Plant Sci 20(5):309–317. https://doi.org/10.1016/j.tplants.02.004

    Article  CAS  PubMed  Google Scholar 

  • Liu X, Ding W, Jiang H (2017) Engineering microbial cell factories for the production of plant natural products: from design principles to industrial-scale production. Microb Cell Fact 16(1):125. https://doi.org/10.1186/s12934-017-0732-7

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ma X, Zhang Q, Zhu Q, Liu W, Chen Y, Qiu R, Wang B, Yang Z, Li H, Lin Y, Xie Y, Shen R, Chen S, Wang Z, Chen Y, Guo J, Chen L, Zhao X, Dong Z, Liu YG (2015) A robust CRISPR/Cas9 system for convenient, high-efficiency multiplex genome editing in monocot and dicot plants. Mol Plant 8(8):1274–1284. https://doi.org/10.1016/j.molp.2015.04.007

    Article  CAS  PubMed  Google Scholar 

  • Maeda H, Dudareva N (2012) The shikimate pathway and aromatic amino acid biosynthesis in plants. Annu Rev Plant Biol 63:73–105

    Article  CAS  PubMed  Google Scholar 

  • Mccarty NS, Ledesma-Amaro R (2019) Synthetic biology tools to engineer microbial communities for biotechnology. Trends Biotechnol 37(2):181–197. https://doi.org/10.1016/j.tibtech.2018.11.002

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • McGarvey DJ, Croteau R (1995) Terpenoid metabolism. Plant Cell 7:1015–1026

    CAS  PubMed  PubMed Central  Google Scholar 

  • Minx J, Lamb W, Callaghan M, Fuss S, Hilaire J, Creutzig F, Amann T, Beringer T, Garcia W, Hartmann J, Khanna T, Lenzi D, Luderer G, Nemet G, Rogelj J, Smith P, Vicente Vicente J, Wilcox J, del Mar Zamora Dominguez M (2018) Negative emissions: Part 1—research landscape and synthesis. Environ Res Lett 13:063001. https://doi.org/10.1088/1748-9326/aabf9b

    Article  Google Scholar 

  • Mitchell W (2011) Natural products from synthetic biology. Curr Opin Chem Biol 15(4):505–515. https://doi.org/10.1016/j.cbpa.2011.05.017

    Article  CAS  PubMed  Google Scholar 

  • Miyao M, Masumoto C, Miyazawa S-I, Fukayama H (2011) Lessons from engineering a single-cell C4 photosynthetic pathway into rice. J Exp Bot 62:3021–3029

    Article  CAS  PubMed  Google Scholar 

  • Mortimer JC (2019) Plant synthetic biology could drive a revolution in biofuels and medicine. Exp Biol Med (Maywood) 244(4):323–331. https://doi.org/10.1177/1535370218793890

    Article  CAS  Google Scholar 

  • Moses T, Pollier J, Thevelein JM, Goossens A (2013) Bioengineering of plant (tri)terpenoids: from metabolic engineering of plants to synthetic biology in vivo and in vitro. New Phytol 200:27–43

    Article  CAS  PubMed  Google Scholar 

  • Neuman K-H, Kumar A, Imani J (2020) Plant cell and tissue culture—a tool in biotechnology. Basics and applications. Springer, Cham, p 459

    Google Scholar 

  • Nguyen H, Abramov M, Eremeeva E, Herdewijn P (2020) In vivo expression of genetic information from phosphoramidate-DNA. Chembiochem 21(1–2):272–278. https://doi.org/10.1002/cbic.201900712

    Article  CAS  PubMed  Google Scholar 

  • Paddon CJ, Westfall PJ, Pitera DJ, Benjamin K, Fisher K, McPhee D, Leavell MD, Tai A, Main A, Eng D et al (2013) High-level semi-synthetic production of the potent antimalarial artemisinin. Nature 496:528–532

    Article  CAS  PubMed  Google Scholar 

  • Patron NJ, Orzaez D, Marillonnet S, Warzecha H, Matthewman C, Youles M, Raitskin O, Leveau A, Farre G, Rogers C, Smith A, Hibberd J, Webb AA, Locke J, Schornack S, Ajioka J, Baulcombe DC, Zipfel C, Kamoun S, Jones JD, Kuhn H, Robatzek S, Van Esse HP, Sanders D, Oldroyd G, Martin C, Field R, O'Connor S, Fox S, Wulff B, Miller B, Breakspear A, Radhakrishnan G, Delaux PM, Loque D, Granell A, Tissier A, Shih P, Brutnell TP, Quick WP, Rischer H, Fraser PD, Aharoni A, Raines C, South PF, Ane JM, Hamberger BR, Langdale J, Stougaard J, Bouwmeester H, Udvardi M, Murray JA, Ntoukakis V, Schafer P, Denby K, Edwards KJ, Osbourn A, Haseloff J (2015) Standards for plant synthetic biology: a common syntax for exchange of DNA parts. New Phytol 208:13–19

    Article  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

    Article  PubMed  CAS  Google Scholar 

  • Petzold CJ, Chan LJ, Nhan M, Adams PD (2015) Analytics for metabolic engineering. Front Bioeng Biotechnol 3:135

    Article  PubMed  PubMed Central  Google Scholar 

  • Pingali PL (2012) Green revolution: impacts, limits, and the path ahead. Proc Natl Acad Sci U S A 109:12302–12308

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pouvreau B, Vanhercke T, Singh S (2018) From plant metabolic engineering to plant synthetic biology: the evolution of the design/build/test/learn cycle. Plant Sci 273:3–12. https://doi.org/10.1016/j.plantsci.2018.03.035

    Article  CAS  PubMed  Google Scholar 

  • Raina A, Sahu PK, Laskar RA, Rajora N, Sao R, Khan S, Ganai RA (2021) Mechanisms of genome maintenance in plants: playing it safe with breaks and bumps. Front Genet 12:861. https://doi.org/10.3389/fgene.2021.675686

    Article  CAS  Google Scholar 

  • Ralph J, Lapierre C, Boerjan W (2019) Lignin structure and its engineering. Curr Opin Biotechnol 56:240–249

    Article  CAS  PubMed  Google Scholar 

  • Reguera G (2011) When microbial conversations get physical. Trends Microbiol 19(3):105–113. https://doi.org/10.1016/j.tim.2010.12.007

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ro D-K, Paradise EM, Ouellet M, Fisher KJ, Newman KL, Ndungu JM, Ho KA, Eachus RA, Ham TS, Kirby J et al (2006) Production of the antimalarial drug precursor artemisinic acid in engineered yeast. Nature 440:940–943

    Article  CAS  PubMed  Google Scholar 

  • Rong YS, Golic KG (2020) Gene targeting by homologous recombination in Drosophila. Science 288:2013–2018. https://doi.org/10.1126/science.288.5473.2013

    Article  Google Scholar 

  • Rosales-Calderon O, Arantes V (2019) A review on commercial-scale high-value products that can be produced alongside cellulosic ethanol. Biotechnol Biofuels 12:240

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Roy A, Kumar A (2013) Pretreatment methods of lignocellulosic materials for biofuel production: a review. J Emerg Trends Eng Appl Sci 4(2):181–193

    Google Scholar 

  • Sharma P, Gaur VK, Kim S-H, Pandey A (2020) Microbial strategies for bio-transforming food waste into resources. Bioresour Technol 299:122580. https://doi.org/10.1016/j.biortech.2019.122580

    Article  CAS  PubMed  Google Scholar 

  • Shih PM (2018) Towards a sustainable bio-based economy: redirecting primary metabolism to new products with plant synthetic biology. Plant Sci Int J Exp Plant Biol 273:84–91. https://doi.org/10.1016/j.plantsci.2018.03.012

    Article  CAS  Google Scholar 

  • Shih PM, Liang Y, Loqué D (2016a) Biotechnology and synthetic biology approaches for metabolic engineering of bioenergy crops. Plant J 87(1):103–117. https://doi.org/10.1111/tpj.13176

    Article  PubMed  Google Scholar 

  • Shih PM, Vuu K, Mansoori N, Ayad L, Louie KB, Bowen BP, Northen TR, Loque D (2016b) A robust gene-stacking method utilizing yeast assembly for plant synthetic biology. Nat Commun 7:13215

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Somerville C, Youngs H, Taylor C, Davis SC, Long SP (2010) Feedstocks for lignocellulosic biofuels. Science 329:790–792

    Article  CAS  PubMed  Google Scholar 

  • Sonoda E, Hochegger H, Saberi A, Taniguchi Y, Takeda S (2006) Differential usage of non- homologous end-joining and homologous recombination in double strand break repair. DNA Repair (Amst) 5(9–10):1021–1029. https://doi.org/10.1016/j.dnarep.2006.05.022

    Article  CAS  Google Scholar 

  • Tatsis EC, O’Connor SE (2016) New developments in engineering plant metabolic pathways. Curr Opin Biotechnol 42:126–132

    Article  CAS  PubMed  Google Scholar 

  • Taylor SH, Hulme SP, Rees M, Ripley BS, Woodward FI, Osborne CP (2010) Ecophysiological traits in C3 and C4 grasses: a phylogenetically controlled screening experiment. New Phytol 185(3):780–791

    Article  CAS  PubMed  Google Scholar 

  • Tong W-Y (2013) Biotransformation of terpenoids and steroids. In: Ramawat KG, Mérillon J-M (eds) Natural products: phytochemistry, botany and metabolism of alkaloids, phenolics and terpenes. Springer, Berlin, pp 2733–2759

    Chapter  Google Scholar 

  • Tzin V, Galili G (2010) New insights into the shikimate and aromatic amino acids biosynthesis pathways in plants. Mol Plant 3:956–972

    Article  CAS  PubMed  Google Scholar 

  • Usmani Z, Sharma M, Sudheer S, Gupta VK, Bhat R (2020) Engineered microbes for pigment production using waste biomass. Curr Genomics 21(2):80–95. https://doi.org/10.2174/1389202921999200330152007

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Vanholme R, Demedts B, Morreel K, Ralph J, Boerjan W (2010) Lignin biosynthesis and structure. Plant Physiol 153:895–905

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Vanholme R, Morreel K, Darrah C, Oyarce P, Grabber JH, Ralph J, Boerjan W (2012) Metabolic engineering of novel lignin in biomass crops. New Phytol 196:978–1000. https://doi.org/10.1111/j.1469-8137.2012.04337.x

    Article  CAS  PubMed  Google Scholar 

  • Vanholme R, Storme V, Vanholme B, Sundin L, Christensen JH, Goeminne G, Halpin C, Rohde A, Morreel K, Boerjan W (2012a) A systems biology view of responses to lignin biosynthesis perturbations in Arabidopsis. Plant Cell 24:3506–3529

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Vickers CE, Bongers M, Liu Q, Delatte T, Bouwmeester H (2014) Metabolic engineering of volatile isoprenoids in plants and microbes. Plant Cell Environ 37:1753–1775

    Article  CAS  PubMed  Google Scholar 

  • Wang P, Dudareva N, Morgan JA, Chapple C (2015) Genetic manipulation of lignocellulosic biomass for bioenergy. Curr Opin Chem Biol 29:32–39. https://doi.org/10.1016/j.cbpa.2015.08.006

    Article  CAS  PubMed  Google Scholar 

  • Wang Q, Quan S, Xiao H (2019) Towards efficient terpenoid biosynthesis: manipulating IPP and DMAPP supply. Bioresour Bioprocess 6:6

    Article  CAS  Google Scholar 

  • WHO (2015) World malaria report. http://www.who.int/malaria/publications/world-malaria-report-2015/report/en/

  • Williamson P (2016) Scrutinize CO2 removal methods. Nature 530:153–155

    Article  CAS  PubMed  Google Scholar 

  • Winchester N, Reilly JM (2019) The economic and emissions benefits of engineered wood products in a low-carbon future. Energy Econ 85:104596. https://doi.org/10.1016/j.eneco.2019.104596

    Article  Google Scholar 

  • Wright RC, Nemhauser J (2019) Plant synthetic biology: quantifying the―known unknowns and discovering the―unknown unknowns. Plant Physiol 179:885–893

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xu S, Ottinger SL, Schaeffer SM et al (2019) Effects of field-grown transgenic switchgrass carbon inputs on soil organic carbon cycling. Peer J 7:e7887. https://doi.org/10.7717/peerj.7887

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yang F, Mitra P, Zhang L, Prak L, Verhertbruggen Y, Kim JS, Sun L, Zheng K, Tan K, Auer M, Scheller HV, Loqué D (2013) Engineering secondary cell wall deposition in plants. Plant Biotechnol J 11(3):325–335. https://doi.org/10.1111/pbi.12016

    Article  CAS  PubMed  Google Scholar 

  • Yu H, Zhao Y (2019) Fluorescence marker-assisted isolation of Cas9-free and CRISPR-edited Arabidopsis plants. In: Qi Y (ed) Plant genome editing with CRISPR systems. Methods in molecular biology, vol 1917. Humana Press, New York. https://doi.org/10.1007/978-1-4939-8991-1_11

  • Zhang H, Zhang J, Wei P, Zhang B, Gou F, Feng Z, Mao Y, Yang L, Zhang H, Xu N, Zhu JK (2014) The CRISPR/Cas9 system produces specific and homozygous targeted gene editing in rice in one generation. Plant Biotechnol J 12(6):797–807. https://doi.org/10.1111/pbi.12200. Epub 2014 May 23

    Article  CAS  PubMed  Google Scholar 

  • Zhao Q, Dixon RA (2011) Transcriptional networks for lignin biosynthesis: more complex than we thought? Trends Plant Sci 16:227–233

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

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

    Ashwani Kumar

  2. Faculty of Medicine, University of Colombo, Colombo, Sri Lanka

    Chamindri Witharana

  3. Dr. B. L. Institute of Biotechnology, Jaipur, India

    Sudipti Arora

  4. Department of Biotechnology, Dr. B. L. Institute of Biotechnology, Jaipur, India

    Sonika Saxena

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

    Yuan-Yeu Yau

Authors
  1. Ashwani Kumar
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Chamindri Witharana
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Sudipti Arora
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Sonika Saxena
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Yuan-Yeu Yau
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Department of Biotechnology, Dr. B. Lal Institute of Biotechnology, Jaipur, Rajasthan, India

    Sudipti Arora

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

    Ashwani Kumar

  3. Department of Local Resources and Department of Life Sciences, Prefectural University of Hiroshima, Hiroshima, Japan

    Shinjiro Ogita

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

    Yuan -Yeu Yau

Rights and permissions

Reprints and permissions

Copyright information

© 2022 The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd.

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Kumar, A., Witharana, C., Arora, S., Saxena, S., Yau, YY. (2022). Metabolic Engineering and Synthetic and Semi-Synthetic Pathways: Biofuel Production for Climate Change Mitigation. In: Arora, S., Kumar, A., Ogita, S., Yau, Y.Y. (eds) Biotechnological Innovations for Environmental Bioremediation. Springer, Singapore. https://doi.org/10.1007/978-981-16-9001-3_6

Download citation

Publish with us

Policies and ethics

Search

Navigation