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Engineering the cellulolytic extreme thermophile Caldicellulosiruptor bescii to reduce carboxylic acids to alcohols using plant biomass as the energy source

  • Bioenergy/Biofuels/Biochemicals - Original Paper
  • Published:
Journal of Industrial Microbiology & Biotechnology

Abstract

Caldicellulosiruptor bescii is the most thermophilic cellulolytic organism yet identified (Topt 78 °C). It grows on untreated plant biomass and has an established genetic system thereby making it a promising microbial platform for lignocellulose conversion to bio-products. Here, we investigated the ability of engineered C. bescii to generate alcohols from carboxylic acids. Expression of aldehyde ferredoxin oxidoreductase (aor from Pyrococcus furiosus) and alcohol dehydrogenase (adhA from Thermoanaerobacter sp. X514) enabled C. bescii to generate ethanol from crystalline cellulose and from biomass by reducing the acetate produced by fermentation. Deletion of lactate dehydrogenase in a strain expressing the AOR–Adh pathway increased ethanol production. Engineered strains also converted exogenously supplied organic acids (isobutyrate and n-caproate) to the corresponding alcohol (isobutanol and hexanol) using both crystalline cellulose and switchgrass as sources of reductant for alcohol production. This is the first instance of an acid to alcohol conversion pathway in a cellulolytic microbe.

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References

  1. Agbor VB, Cicek N, Sparling R, Berlin A, Levin DB (2011) Biomass pretreatment: Fundamentals toward application. Biotechnol Adv 29:675–685. https://doi.org/10.1016/j.biotechadv.2011.05.005

    Article  CAS  PubMed  Google Scholar 

  2. Aono S, Bryant FO, Adams MW (1989) A novel and remarkably thermostable ferredoxin from the hyperthermophilic archaebacterium Pyrococcusfuriosus. J Bacteriol 171:3433–3439. https://doi.org/10.1128/jb.171.6.3433-3439.1989

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Atsumi S, Hanai T, Liao JC (2008) Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels. Nature 451:86–89. https://doi.org/10.1038/nature06450

    Article  CAS  PubMed  Google Scholar 

  4. Baez A, Cho K-M, Liao JC (2011) High-flux isobutanol production using engineered Escherichiacoli: a bioreactor study with in situ product removal. Appl Microbiol Biotechnol 90:1681–1690. https://doi.org/10.1007/s00253-011-3173-y

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Basen M, Rhaesa AM, Kataeva I, Prybol CJ, Scott IM, Poole FL, Adams MWW (2014) Degradation of high loads of crystalline cellulose and of unpretreated plant biomass by the thermophilic bacterium Caldicellulosiruptorbescii. Bioresour Technol 152:384–392. https://doi.org/10.1016/j.biortech.2013.11.024

    Article  CAS  PubMed  Google Scholar 

  6. Basen M, Schut GJ, Nguyen DM, Lipscomb GL, Benn RA, Prybol CJ, Vaccaro BJ, Poole FL, Kelly RM, Adams MW (2014) Single gene insertion drives bioalcohol production by a thermophilic archaeon. Proc Natl Acad Sci 111:17618–17623. https://doi.org/10.1073/pnas.1413789111

    Article  CAS  PubMed  Google Scholar 

  7. Biswas R, Prabhu S, Lynd LR, Guss AM (2014) Increase in ethanol yield via elimination of lactate production in an ethanol-tolerant mutant of Clostridiumthermocellum. PLoS ONE 9:e86389. https://doi.org/10.1371/journal.pone.0086389

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Blumer-Schuette SE, Brown SD, Sander KB, Bayer EA, Kataeva I, Zurawski JV, Conway JM, Adams MWW, Kelly RM (2014) Thermophilic lignocellulose deconstruction. FEMS Microbiol Rev 38:393–448. https://doi.org/10.1111/1574-6976.12044

    Article  CAS  PubMed  Google Scholar 

  9. Carere CR, Rydzak T, Verbeke TJ, Cicek N, Levin DB, Sparling R (2012) Linking genome content to biofuel production yields: a meta-analysis of major catabolic pathways among select H2 and ethanol-producing bacteria. BMC Microbiol. https://doi.org/10.1186/1471-2180-12-295

    Article  PubMed  PubMed Central  Google Scholar 

  10. Cha M, Chung D, Elkins JG, Guss AM, Westpheling J (2013) Metabolic engineering of Caldicellulosiruptorbescii yields increased hydrogen production from lignocellulosic biomass. Biotechnol Biofuels 6:1–8. https://doi.org/10.1186/1754-6834-6-85

    Article  CAS  Google Scholar 

  11. Cha M, Wang H, Chung D, Bennetzen JL, Westpheling J (2013) Isolation and bioinformatic analysis of a novel transposable element, ISCbe4, from the hyperthermophilic bacterium, Caldicellulosiruptorbescii. J Ind Microbiol Biotechnol 40:1443–1448. https://doi.org/10.1007/s10295-013-1345-8

    Article  CAS  PubMed  Google Scholar 

  12. Cheng C, Li W, Lin M, Yang S-T (2019) Metabolic engineering of Clostridium carboxidivorans for enhanced ethanol and butanol production from syngas and glucose. Bioresour Technol 284:415–423. https://doi.org/10.1016/j.biortech.2019.03.145

    Article  CAS  PubMed  Google Scholar 

  13. Chockalingam SR, Saravanan G (2011) Influence of hexanol-diesel blends on constant speed diesel engine. Thermal Sci 15:1215–1222. https://doi.org/10.2298/TSCI101001089S

    Article  Google Scholar 

  14. Chung D, Cha M, Farkas J, Westpheling J (2013) Construction of a stable replicating shuttle vector for Caldicellulosiruptor species: use for extending genetic methodologies to other members of this genus. PLoS ONE 8:e62881. https://doi.org/10.1371/journal.pone.0062881

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Chung D, Cha M, Guss AM, Westpheling J (2014) Direct conversion of plant biomass to ethanol by engineered Caldicellulosiruptorbescii. Proc Natl Acad Sci 111:8931–8936. https://doi.org/10.1073/pnas.1402210111

    Article  CAS  PubMed  Google Scholar 

  16. Chung D, Cha M, Snyder EN, Elkins JG, Guss AM, Westpheling J (2015) Cellulosic ethanol production via consolidated bioprocessing at 75 °C by engineered Caldicellulosiruptorbescii. Biotechnol Biofuels 8:1–13. https://doi.org/10.1186/s13068-015-0346-4

    Article  CAS  Google Scholar 

  17. Chung D, Farkas J, Huddleston JR, Olivar E, Westpheling J (2012) Methylation by a unique α-class N4-cytosine methyltransferase is required for DNA transformation of Caldicellulosiruptorbescii DSM6725. PLoS ONE 7:e43844. https://doi.org/10.1371/journal.pone.0043844

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Chung D, Farkas J, Westpheling J (2013) Overcoming restriction as a barrier to DNA transformation in Caldicellulosiruptor species results in efficient marker replacement. Biotechnol Biofuels 6:1. https://doi.org/10.1186/1754-6834-6-82

    Article  CAS  Google Scholar 

  19. Dale BE (2015) A new industry has been launched: the cellulosic biofuels ship (finally) sails. Biofuels Bioprod Biorefin 9:1–3. https://doi.org/10.1002/bbb.1532

    Article  CAS  Google Scholar 

  20. Dam P, Kataeva I, Yang S-J, Zhou F, Yin Y, Chou W, Poole FL, Westpheling J, Hettich R, Giannone R, Lewis DL, Kelly R, Gilbert HJ, Henrissat B, Xu Y, Adams MWW (2011) Insights into plant biomass conversion from the genome of the anaerobic thermophilic bacterium Caldicellulosiruptorbescii DSM 6725. Nucleic Acids Res 39:3240–3254. https://doi.org/10.1093/nar/gkq1281

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Dias AA, Pinto PA, Fraga I, Bezerra RMF (2014) Diagnosis of enzyme inhibition using excel solver: a combined dry and wet laboratory exercise. J Chem Educ 91:1017–1021. https://doi.org/10.1021/ed3006677

    Article  CAS  Google Scholar 

  22. Greenwell HC, Lloyd-Evans M, Wenner C (2013) Biofuels, science and society. Interface Focus 3:1–4. https://doi.org/10.1098/rsfs.2012.0093

    Article  Google Scholar 

  23. Gronenberg LS, Marcheschi RJ, Liao JC (2013) Next generation biofuel engineering in prokaryotes. Curr Opin Chem Biol 17:462–471. https://doi.org/10.1016/j.cbpa.2013.03.037

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Grootscholten TIM, Strik DPBTB, Steinbusch KJJ, Buisman CJN, Hamelers HVM (2014) Two-stage medium chain fatty acid (MCFA) production from municipal solid waste and ethanol. Appl Energy 116:223–229. https://doi.org/10.1016/j.apenergy.2013.11.061

    Article  CAS  Google Scholar 

  25. Hitschler L, Kuntz M, Langschied F, Basen M (2018) Thermoanaerobacter species differ in their potential to reduce organic acids to their corresponding alcohols. Appl Microbiol Biotechnol 102:8465–8476. https://doi.org/10.1007/s00253-018-9210-3

    Article  CAS  PubMed  Google Scholar 

  26. Isom CE, Nanny MA, Tanner RS (2015) Improved conversion efficiencies for n-fatty acid reduction to primary alcohols by the solventogenic acetogen Clostridiumragsdalei. J Ind Microbiol Biotechnol 42:29–38. https://doi.org/10.1007/s10295-014-1543-z

    Article  CAS  PubMed  Google Scholar 

  27. Keller MW, Lipscomb GL, Nguyen DM, Crowley AT, Schut GJ, Scott I, Kelly RM, Adams MWW (2017) Ethanol production by the hyperthermophilic archaeon Pyrococcusfuriosus by expression of bacterial bifunctional alcohol dehydrogenases. Microb Biotechnol 10:1535–1545. https://doi.org/10.1111/1751-7915.12486

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Kucek LA, Nguyen M, Angenent LT (2016) Conversion of l-lactate into n-caproate by a continuously fed reactor microbiome. Water Res 93:163–171. https://doi.org/10.1016/j.watres.2016.02.018

    Article  CAS  PubMed  Google Scholar 

  29. Lee LL, Crosby JR, Rubinstein GM, Laemthong T, Bing RG, Straub CT, Adams MWW, Kelly RM (2020) The biology and biotechnology of the genus Caldicellulosiruptor: recent developments in ‘Caldi World’. Extremophiles 24:1–15. https://doi.org/10.1007/s00792-019-01116-5

    Article  CAS  PubMed  Google Scholar 

  30. Lipscomb GL, Conway JM, Blumer-Schuette SE, Kelly RM, Adams MWW (2016) A highly thermostable kanamycin resistance marker expands the tool kit for genetic manipulation of Caldicellulosiruptorbescii. Appl Environ Microbiol 82:4421–4428. https://doi.org/10.1128/aem.00570-16

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Lu J, Brigham CJ, Gai CS, Sinskey AJ (2012) Studies on the production of branched-chain alcohols in engineered Ralstoniaeutropha. Appl Microbiol Biotechnol 96:283–297. https://doi.org/10.1007/s00253-012-4320-9

    Article  CAS  PubMed  Google Scholar 

  32. Lynd LR, Van Zyl WH, McBride JE, Laser M (2005) Consolidated bioprocessing of cellulosic biomass: an update. Curr Opin Biotechnol 16:577–583. https://doi.org/10.1016/j.copbio.2005.08.009

    Article  CAS  PubMed  Google Scholar 

  33. Lynd LR, Weimer PJ, van Zyl WH, Pretorius IS (2002) Microbial cellulose utilization: fundamentals and biotechnology. Microbiol Mol Biol Rev 66:506–577. https://doi.org/10.1128/MMBR.66.3.506-577.2002(table of contents)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Mann J, Yao N, Bocarsly AB (2006) Characterization and analysis of new catalysts for a direct ethanol fuel cell. Langmuir 22:10432–10436. https://doi.org/10.1021/la061200c

    Article  CAS  PubMed  Google Scholar 

  35. Mock J, Zheng Y, Mueller AP, Ly S, Tran L, Segovia S, Nagaraju S, Kopke M, Durre P, Thauer RK (2015) Energy conservation associated with ethanol formation from H2 and CO2 in Clostridiumautoethanogenum involving electron bifurcation. J Bacteriol 197:2965–2980. https://doi.org/10.1128/jb.00399-15

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Mukund S, Adams MW (1991) The novel tungsten-iron-sulfur protein of the hyperthermophilic archaebacterium, Pyrococcusfuriosus, is an aldehyde ferredoxin oxidoreductase. Evidence for its participation in a unique glycolytic pathway. J Biol Chem 266:14208–14216

    CAS  PubMed  Google Scholar 

  37. Nguyen DMN, Schut GJ, Zadvornyy OA, Tokmina-Lukaszewska M, Poudel S, Lipscomb GL, Adams LA, Dinsmore JT, Nixon WJ, Boyd ES, Bothner B, Peters JW, Adams MWW (2017) Two functionally distinct NADP+-dependent ferredoxin oxidoreductases maintain the primary redox balance of Pyrococcusfuriosus. J Biol Chem 292:14603–14616. https://doi.org/10.1074/jbc.M117.794172

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Nissen LS, Basen M (2019) The emerging role of aldehyde:ferredoxin oxidoreductases in microbially-catalyzed alcohol production. J Biotechnol 306:105–117. https://doi.org/10.1016/j.jbiotec.2019.09.005

    Article  CAS  PubMed  Google Scholar 

  39. Olson DG, McBride JE, Shaw AJ, Lynd LR (2012) Recent progress in consolidated bioprocessing. Curr Opin Biotechnol 23:396–405. https://doi.org/10.1016/j.copbio.2011.11.026

    Article  CAS  PubMed  Google Scholar 

  40. Olson DG, Sparling R, Lynd LR (2015) Ethanol production by engineered thermophiles. Curr Opin Biotechnol 33:130–141. https://doi.org/10.1016/j.copbio.2015.02.006

    Article  CAS  PubMed  Google Scholar 

  41. Parisutham V, Kim TH, Lee SK (2014) Feasibilities of consolidated bioprocessing microbes: from pretreatment to biofuel production. Bioresour Technol 161:431–440. https://doi.org/10.1016/j.biortech.2014.03.114

    Article  CAS  PubMed  Google Scholar 

  42. Perez JM, Richter H, Loftus SE, Angenent LT (2013) Biocatalytic reduction of short-chain carboxylic acids into their corresponding alcohols with syngas fermentation. Biotechnol Bioeng 110:1066–1077. https://doi.org/10.1002/bit.24786

    Article  CAS  PubMed  Google Scholar 

  43. Roddy DJ (2013) Biomass in a petrochemical world. Interface Focus 3:20120038. https://doi.org/10.1098/rsfs.2012.0038

    Article  PubMed  PubMed Central  Google Scholar 

  44. Schut GJ, Adams MWW (2009) The iron-hydrogenase of Thermotogamaritima utilizes ferredoxin and NADH synergistically: a new perspective on anaerobic hydrogen production. J Bacteriol 191:4451–4457. https://doi.org/10.1128/jb.01582-08

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Scott IM, Rubinstein GM, Lipscomb GL, Basen M, Schut GJ, Rhaesa AM, Lancaster WA, Poole FL, Kelly RM, Adams MWW (2015) A new class of tungsten-containing oxidoreductase in the genus of the plant biomass-degrading, thermophilic bacteria Caldicellulosiruptor. Appl Environ Microbiol 81:7339–7347. https://doi.org/10.1128/aem.01634-15

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Scully SM, Orlygsson J (2020) Branched-chain amino acid catabolism of Thermoanaerobacter pseudoethanolicus reveals potential route to branched-chain alcohol formation. Extremophiles 24:121–133. https://doi.org/10.1007/s00792-019-01140-5

    Article  CAS  PubMed  Google Scholar 

  47. Sun X, Atiyeh HK, Kumar A, Zhang H (2018) Enhanced ethanol production by Clostridium ragsdalei from syngas by incorporating biochar in the fermentation medium. Bioresour Technol 247:291–301. https://doi.org/10.1016/j.biortech.2017.09.060

    Article  CAS  PubMed  Google Scholar 

  48. Wang S, Huang H, Moll J, Thauer RK (2010) NADP+ reduction with reduced ferredoxin and NADP+ reduction with NADH are coupled via an electron-bifurcating enzyme complex in Clostridiumkluyveri. J Bacteriol 192:5115–5123. https://doi.org/10.1128/jb.00612-10

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Williams-Rhaesa AM, Poole FL, Dinsmore JT, Lipscomb GL, Rubinstein GM, Scott IM, Conway JM, Lee LL, Khatibi PA, Kelly RM, Adams MWW (2017) Genome stability in engineered strains of the extremely thermophilic, lignocellulose-degrading bacterium Caldicellulosiruptorbescii. Appl Environ Microbiol 83:e00444-00417. https://doi.org/10.1128/aem.00444-17

    Article  CAS  Google Scholar 

  50. Williams-Rhaesa AM, Rubinstein GM, Scott IM, Lipscomb GL, Poole IIFL, Kelly RM, Adams MWW (2018) Engineering redox-balanced ethanol production in the cellulolytic and extremely thermophilic bacterium, Caldicellulosiruptor bescii. Metab Eng Commun 7:e00073. https://doi.org/10.1016/j.mec.2018.e00073

    Article  PubMed  PubMed Central  Google Scholar 

  51. Wyman CE, Dale BE, Elander RT, Holtzapple M, Ladisch MR, Lee YY (2005) Coordinated development of leading biomass pretreatment technologies. Bioresour Technol 96:1959–1966. https://doi.org/10.1016/j.biortech.2005.01.010

    Article  CAS  PubMed  Google Scholar 

  52. Yang S-J, Kataeva I, Hamilton-Brehm SD, Engle NL, Tschaplinski TJ, Doeppke C, Davis M, Westpheling J, Adams MW (2009) Efficient degradation of lignocellulosic plant biomass, without pretreatment, by the thermophilic anaerobe Anaerocellumthermophilum DSM 6725. Appl Environ Microbiol 75:4762–4769. https://doi.org/10.1128/aem.00236-09

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Yang S-J, Kataeva I, Wiegel J, Yin Y, Dam P, Xu Y, Westpheling J, Adams MWW (2010) Classification of 'Anaerocellumthermophilum' strain DSM 6725 as Caldicellulosiruptorbescii sp. nov. Int J Syst Evol Microbiol 60:2011–2015. https://doi.org/10.1099/ijs.0.017731-0

    Article  PubMed  Google Scholar 

  54. Zeldes BM, Straub CT, Otten JK, Adams MWW, Kelly RM (2018) A synthetic enzymatic pathway for extremely thermophilic acetone production based on the unexpectedly thermostable acetoacetate decarboxylase from Clostridiumacetobutylicum. Biotechnol Bioeng 115:2951–2961. https://doi.org/10.1002/bit.26829

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Zhang F, Rodriguez S, Keasling JD (2011) Metabolic engineering of microbial pathways for advanced biofuels production. Curr Opin Biotechnol 22:775–783. https://doi.org/10.1016/j.copbio.2011.04.024

    Article  CAS  PubMed  Google Scholar 

  56. Zhu X, Tao Y, Liang C, Li X, Wei N, Zhang W, Zhou Y, Yang Y, Bo T (2015) The synthesis of n-caproate from lactate: a new efficient process for medium-chain carboxylates production. Sci Rep 5:e14360. https://doi.org/10.1038/srep14360

    Article  CAS  Google Scholar 

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Acknowledgements

This material is based on work supported by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research (DE-SC0019391) and by a grant (DE-PS02-06ER64304) from the Bioenergy Science Center at Oak Ridge National Laboratory. We thank Israel Scott, Laura Lee, Piyum Khatibi, Jeff Zurawski, Jonathan Conway, Diep Nguyen, Farris Poole, Mirko Basen, and Matthew Keller for helpful discussions, and Daewhan Chung and Janet Westpheling for providing C. bescii strain JWCB018 and plasmids pDCW121 and pDCW88.

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Rubinstein, G.M., Lipscomb, G.L., Williams-Rhaesa, A.M. et al. Engineering the cellulolytic extreme thermophile Caldicellulosiruptor bescii to reduce carboxylic acids to alcohols using plant biomass as the energy source. J Ind Microbiol Biotechnol 47, 585–597 (2020). https://doi.org/10.1007/s10295-020-02299-z

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