Genome-Scale Modeling of Thermophilic Microorganisms

  • Sanjeev DahalEmail author
  • Suresh Poudel
  • R. Adam Thompson
Part of the Advances in Biochemical Engineering/Biotechnology book series (ABE, volume 160)


Thermophilic microorganisms are of increasing interest for many industries as their enzymes and metabolisms are highly efficient at elevated temperatures. However, their metabolic processes are often largely different from their mesophilic counterparts. These differences can lead to metabolic engineering strategies that are doomed to fail. Genome-scale metabolic modeling is an effective and highly utilized way to investigate cellular phenotypes and to test metabolic engineering strategies. In this review we chronicle a number of thermophilic organisms that have recently been studied with genome-scale models. The microorganisms spread across archaea and bacteria domains, and their study gives insights that can be applied in a broader context than just the species they describe. We end with a perspective on the future development and applications of genome-scale models of thermophilic organisms.


Draft reconstruction Flux balance analysis Flux variability analysis Gap-filling Genome-scale models Stoichiometric matrix 


  1. 1.
    Brock TD (1985) Life at high temperatures. Science 230:132–138CrossRefGoogle Scholar
  2. 2.
    Brock TD, Freeze H (1969) Thermus aquaticus gen. n. and sp. n., a nonsporulating extreme thermophile. J Bacteriol 98(1):289–297Google Scholar
  3. 3.
    Bult CJ, White O, Olsen GJ, Zhou L (1996) Complete genome sequence of the methanogenic archaeon. Methanococcus jannaschii. Science 273:1058CrossRefGoogle Scholar
  4. 4.
    Brock TD (1967) Life at high temperatures. Science 158:1012–1019CrossRefGoogle Scholar
  5. 5.
    Robb F, Antranikian G, Grogan D, Driessen A (2007) Thermophiles: biology and technology at high temperatures. CRC PressGoogle Scholar
  6. 6.
    Caldwell D, Brannan D, Kieft T (1983) Thermothrix thiopara: selection and adaptation of a filamentous sulfur-oxidizing bacterium colonizing hot spring tufa at pH 7.0 and 74 C. Ecol Bull 38:129–134Google Scholar
  7. 7.
    Zeikus J (1979) Thermophilic bacteria: ecology, physiology and technology. Enzyme Microb Technol 1:243–252CrossRefGoogle Scholar
  8. 8.
    Shelef G, Kimchie S, Grynberg H (1980) High-rate thermophilic anaerobic digestion of agricultural wastes. In Biotechnol Bioeng Symp (United States). Environmental and Water Resources Engineering Dept., Technion, Haifa, IsraelGoogle Scholar
  9. 9.
    Gajalakshmi S, Abbasi S (2008) Solid waste management by composting: state of the art. Crit Rev Environ Sci Technol 38:311–400CrossRefGoogle Scholar
  10. 10.
    Cecchi F, Pavan P, Alvarez JM, Bassetti A, Cozzolino C (1991) Anaerobic digestion of municipal solid waste: thermophilic vs. mesophilic performance at high solids. Waste Manag Res 9:305–315CrossRefGoogle Scholar
  11. 11.
    Micolucci F, Gottardo M, Cavinato C, Pavan P, Bolzonella D (2016) Mesophilic and thermophilic anaerobic digestion of the liquid fraction of pressed biowaste for high energy yields recovery. Waste Manag 48:227–235CrossRefGoogle Scholar
  12. 12.
    Deveci H, Akcil A, Alp I (2004) Bioleaching of complex zinc sulphides using mesophilic and thermophilic bacteria: comparative importance of pH and iron. Hydrometallurgy 73:293–303CrossRefGoogle Scholar
  13. 13.
    Krebs W, Brombacher C, Bosshard PP, Bachofen R, Brandl H (1997) Microbial recovery of metals from solids. FEMS Microbiol Rev 20:605–617CrossRefGoogle Scholar
  14. 14.
    Barrett J (1990) Metal extraction by bacterial oxidation of minerals. HorwoodGoogle Scholar
  15. 15.
    Rossi G (1990) Biohydrometallurgy. McGraw-HillGoogle Scholar
  16. 16.
    Bobadilla-Fazzini RA, Cortés MP, Maass A, Parada P (2014) Sulfobacillus thermosulfidooxidans strain Cutipay enhances chalcopyrite bioleaching under moderate thermophilic conditions in the presence of chloride ion. AMB Express 4:1CrossRefGoogle Scholar
  17. 17.
    Zhang L, Wu J, Wang Y, Wan L, Mao F, Zhang W, Chen X, Zhou H (2014) Influence of bioaugmentation with Ferroplasma thermophilum on chalcopyrite bioleaching and microbial community structure. Hydrometallurgy 146:15–23CrossRefGoogle Scholar
  18. 18.
    Oberhardt MA, Palsson BØ, Papin JA (2009) Applications of genome-scale metabolic reconstructions. Mol Syst Biol 5:320CrossRefGoogle Scholar
  19. 19.
    Varma A, Palsson B (1994) Metabolic flux balancing: basic concepts, scientific and practical use. Nat Biotechnol 12:994–998CrossRefGoogle Scholar
  20. 20.
    Agren R, Liu L, Shoaie S, Vongsangnak W, Nookaew I, Nielsen J (2013) The RAVEN toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysogenum. PLoS Comput Biol 9:e1002980CrossRefGoogle Scholar
  21. 21.
    Schellenberger J, Que R, Fleming RMT, Thiele I, Orth JD, Feist AM, Zielinski DC, Bordbar A, Lewis NE, Rahmanian S et al (2011) Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Nat Protoc 6:1290–1307CrossRefGoogle Scholar
  22. 22.
    King ZA, Lu J, Dräger A, Miller P, Federowicz S, Lerman JA, Ebrahim A, Palsson BO, Lewis NE (2016) BiGG models: a platform for integrating, standardizing and sharing genome-scale models. Nucleic Acids Res 44:D515–D522CrossRefGoogle Scholar
  23. 23.
    Roberts S, Gowen C, Brooks JP, Fong S (2010) Genome-scale metabolic analysis of Clostridium thermocellum for bioethanol production. BMC Syst Biol 4:31CrossRefGoogle Scholar
  24. 24.
    Roberts SB, Gowen CM, Brooks JP, Fong SS (2010) Genome-scale metabolic analysis of Clostridium thermocellum for bioethanol production. BMC Syst Biol 4:1CrossRefGoogle Scholar
  25. 25.
    Milton H, Reddy VJ, Tamang D, Västermark A (2014) The transporter classification database. Nucleic Acids Res 42:251–258CrossRefGoogle Scholar
  26. 26.
    Gowen CM, Fong SS (2010) Genome-scale metabolic model integrated with RNAseq data to identify metabolic states of Clostridium thermocellum. Biotechnol J 5:759–767CrossRefGoogle Scholar
  27. 27.
    Thompson RA, Layton DS, Guss AM, Olson DG, Lynd LR, Trinh CT (2015) Elucidating central metabolic redox obstacles hindering ethanol production in Clostridium thermocellum. Metab Eng 32:207–219CrossRefGoogle Scholar
  28. 28.
    Zhou J, Olson DG, Argyros DA, Deng Y, van Gulik WM, van Dijken JP, Lynd LR (2013) Atypical glycolysis in Clostridium thermocellum. Appl Environ Microbiol 79:3000–3008CrossRefGoogle Scholar
  29. 29.
    Feinberg L, Foden J, Barrett T, Davenport KW, Bruce D, Detter C, Tapia R, Han C, Lapidus A, Lucas S et al (2011) Complete genome sequence of the cellulolytic thermophile Clostridium thermocellum DSM1313. J Bacteriol 193:2906–2907CrossRefGoogle Scholar
  30. 30.
    Tripathi SA, Olson DG, Argyros DA, Miller BB, Barrett TF, Murphy DM, McCool JD, Warner AK, Rajgarhia VB, Lynd LR et al (2010) Development of pyrF-based genetic system for targeted gene deletion in Clostridium thermocellum and creation of a pta mutant. Appl Environ Microbiol 76:6591–6599CrossRefGoogle Scholar
  31. 31.
    Thompson RA, Dahal S, Garcia S, Nookaew I, Trinh CT (2016) Exploring complex cellular phenotypes and model-guided strain design with a novel genome-scale metabolic model of Clostridium thermocellum DSM 1313 implementing an adjustable cellulosome. Biotechnology Biofuels 9:194CrossRefGoogle Scholar
  32. 32.
    Ozaki S, Fujimitsu K, Kurumizaka H, Katayama T (2006) The DnaA homolog of the hyperthermophilic eubacterium Thermotoga maritima forms an open complex with a minimal 149‐bp origin region in an ATP‐dependent manner. Genes Cells 11:425–438CrossRefGoogle Scholar
  33. 33.
    Huber R, Langworthy TA, König H, Thomm M, Woese CR, Sleytr UB, Stetter KO (1986) Thermotoga maritima sp. nov. represents a new genus of unique extremely thermophilic eubacteria growing up to 90°C. Arch Microbiol 144:324–333CrossRefGoogle Scholar
  34. 34.
    Nelson KE, Clayton RA, Gill SR, Gwinn ML, Dodson RJ, Haft DH, Hickey EK, Peterson JD, Nelson WC, Ketchum KA et al (1999) Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima. Nature 399:323–329CrossRefGoogle Scholar
  35. 35.
    Zhang Y, Thiele I, Weekes D, Li Z, Jaroszewski L, Ginalski K, Deacon AM, Wooley J, Lesley SA, Wilson IA (2009) Three-dimensional structural view of the central metabolic network of Thermotoga maritima. Science 325:1544–1549CrossRefGoogle Scholar
  36. 36.
    Jensen RA (1976) Enzyme recruitment in evolution of new function. Annu Rev Microbiol 30:409–425CrossRefGoogle Scholar
  37. 37.
    Nogales J, Gudmundsson S, Thiele I (2012) An in silico re-design of the metabolism in Thermotoga maritima for increased biohydrogen production. Int J Hydrogen Energy 37:12205–12218Google Scholar
  38. 38.
    Lee N-R, Lakshmanan M, Aggarwal S, Song J-W, Karimi IA, Lee D-Y, Park J-B (2014) Genome-scale metabolic network reconstruction and in silico flux analysis of the thermophilic bacterium Thermus thermophilus HB27. Microb Cell Fact 13:1CrossRefGoogle Scholar
  39. 39.
    Kaneda T (1991) Iso-and anteiso-fatty acids in bacteria: biosynthesis, function, and taxonomic significance. Microbiol Rev 55:288–302Google Scholar
  40. 40.
    Nordström KM, Laakso SV (1992) Effect of growth temperature on fatty acid composition of ten thermus strains. Appl Environ Microbiol 58:1656–1660Google Scholar
  41. 41.
    Pask-Hughes RA, Shaw N (1982) Glycolipids from some extreme thermophilic bacteria belonging to the genus Thermus. J Bacteriol 149:54–58Google Scholar
  42. 42.
    Oshima T (2007) Unique polyamines produced by an extreme thermophile, Thermus thermophilus. Amino Acids 33:367–372CrossRefGoogle Scholar
  43. 43.
    Ulas T, Riemer SA, Zaparty M, Siebers B, Schomburg D (2012) Genome-scale reconstruction and analysis of the metabolic network in the hyperthermophilic archaeon Sulfolobus solfataricus. PLoS One 7:e43401CrossRefGoogle Scholar
  44. 44.
    Teufel R, Kung JW, Kockelkorn D, Alber BE, Fuchs G (2009) 3-Hydroxypropionyl-coenzyme A dehydratase and acryloyl-coenzyme A reductase, enzymes of the autotrophic 3-hydroxypropionate/4-hydroxybutyrate cycle in the Sulfolobales. J Bacteriol 191:4572–4581CrossRefGoogle Scholar
  45. 45.
    Berg IA, Kockelkorn D, Ramos-Vera WH, Say RF, Zarzycki J, Hügler M, Alber BE, Fuchs G (2010) Autotrophic carbon fixation in archaea. Nat Rev Microbiol 8:447–460CrossRefGoogle Scholar
  46. 46.
    Quester S, Schomburg D (2011) EnzymeDetector: an integrated enzyme function prediction tool and database. BMC Bioinformatics 12:376CrossRefGoogle Scholar
  47. 47.
    Kanehisa M, Goto S (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28:27–30CrossRefGoogle Scholar
  48. 48.
    Caspi R, Altman T, Billington R, Dreher K, Foerster H, Fulcher CA, Holland TA, Keseler IM, Kothari A, Kubo A (2014) The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res 42:D459–D471CrossRefGoogle Scholar
  49. 49.
    Scheer M, Grote A, Chang A, Schomburg I, Munaretto C, Rother M, Söhngen C, Stelzer M, Thiele J, Schomburg D (2010) BRENDA, the enzyme information system in 2011. Nucleic Acids Res gkq1089Google Scholar
  50. 50.
    Wilson DB (2004) Studies of Thermobifida fusca plant cell wall degrading enzymes. Chem Rec 4:72–82CrossRefGoogle Scholar
  51. 51.
    Deng Y, Fong SS (2011) Metabolic engineering of Thermobifida fusca for direct aerobic bioconversion of untreated lignocellulosic biomass to 1-propanol. Metab Eng 13:570–577CrossRefGoogle Scholar
  52. 52.
    Vanee N, Brooks JP, Spicer V, Shamshurin D, Krokhin O, Wilkins JA, Deng Y, Fong SS (2014) Proteomics-based metabolic modeling and characterization of the cellulolytic bacterium Thermobifida fusca. BMC Syst Biol 8:1CrossRefGoogle Scholar
  53. 53.
    Islam MA, Zengler K, Edwards EA, Mahadevan R, Stephanopoulos G (2015) Investigating Moorella thermoacetica metabolism with a genome-scale constraint-based metabolic model. Integr Biol 7:869–882CrossRefGoogle Scholar
  54. 54.
    Mock J, Wang S, Huang H, Kahnt J, Thauer RK (2014) Evidence for a hexaheteromeric methylenetetrahydrofolate reductase in Moorella thermoacetica. J Bacteriol 196:3303–3314CrossRefGoogle Scholar
  55. 55.
    Schuchmann K, Müller V (2014) Autotrophy at the thermodynamic limit of life: a model for energy conservation in acetogenic bacteria. Nat Rev Microbiol 12:809–821CrossRefGoogle Scholar
  56. 56.
    Hols P, Hancy F, Fontaine L, Grossiord B, Prozzi D, Leblond-Bourget N, Decaris B, Bolotin A, Delorme C, Ehrlich SD (2005) New insights in the molecular biology and physiology of Streptococcus thermophilus revealed by comparative genomics. FEMS Microbiol Rev 29:435–463Google Scholar
  57. 57.
    Currie DH, Raman B, Gowen CM, Tschaplinski TJ, Land ML, Brown SD, Covalla SF, Klingeman DM, Yang ZK, Engle NL (2015) Genome-scale resources for Thermoanaerobacterium saccharolyticum. BMC Syst Biol 9:1CrossRefGoogle Scholar
  58. 58.
    Chelliah V, Juty N, Ajmera I, Ali R, Dumousseau M, Glont M, Hucka M, Jalowicki G, Keating S, Knight-Schrijver V et al (2015) BioModels: ten-year anniversary. Nucleic Acids Res 43:D542–D548CrossRefGoogle Scholar
  59. 59.
    Le Novère N, Bornstein B, Broicher A, Courtot M, Donizelli M, Dharuri H, Li L, Sauro H, Schilstra M, Shapiro B et al (2006) BioModels database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. Nucleic Acids Res 34:D689–D691CrossRefGoogle Scholar
  60. 60.
    Anderson I, Göker M, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng J-F, Tapia R, Han C, Goodwin L et al (2011) Complete genome sequence of the hyperthermophilic chemolithoautotroph Pyrolobus fumarii type strain (1A(T)). Stand Genomic Sci 4:381–392CrossRefGoogle Scholar
  61. 61.
    Robb FT, Maeder DL, Brown JR, DiRuggiero J, Stump MD, Yeh RK, Weiss RB, Dunn DM (2001) Genomic sequence of hyperthermophile, Pyrococcus furiosus: implications for physiology and enzymology. Methods Enzymol 330:134–157CrossRefGoogle Scholar
  62. 62.
    Klenk HP, Clayton RA, Tomb JF, White O, Nelson KE, Ketchum KA, Dodson RJ, Gwinn M, Hickey EK, Peterson JD et al (1997) The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus. Nature 390:364–370CrossRefGoogle Scholar
  63. 63.
    Tsoka S, Simon D, Ouzounis CA (2004) Automated metabolic reconstruction for Methanococcus jannaschii. Archaea 1:223–229CrossRefGoogle Scholar
  64. 64.
    Kawarabayasi Y, Hino Y, Horikawa H, Yamazaki S, Haikawa Y, Jin-no K, Takahashi M, Sekine M, Baba S, Ankai A et al (1999) Complete genome sequence of an aerobic hyper-thermophilic crenarchaeon, Aeropyrum pernix K1. DNA Res 6:83–101, 145–152CrossRefGoogle Scholar
  65. 65.
    Deckert G, Warren PV, Gaasterland T, Young WG, Lenox AL, Graham DE, Overbeek R, Snead MA, Keller M, Aujay M et al (1998) The complete genome of the hyperthermophilic bacterium Aquifex aeolicus. Nature 392:353–358CrossRefGoogle Scholar
  66. 66.
    Brügger K, Chen L, Stark M, Zibat A, Redder P, Ruepp A, Awayez M, She Q, Garrett RA, Klenk H-P (2007) The genome of Hyperthermus butylicus: a sulfur-reducing, peptide fermenting, neutrophilic Crenarchaeote growing up to 108 degrees C. Archaea (Vancouver, BC) 2:127–135Google Scholar
  67. 67.
    Ravin NV, Mardanov AV, Beletsky AV, Kublanov IV, Kolganova TV, Lebedinsky AV, Chernyh NA, Bonch-Osmolovskaya EA, Skryabin KG (2009) Complete genome sequence of the anaerobic, protein-degrading hyperthermophilic crenarchaeon Desulfurococcus kamchatkensis. J Bacteriol 191:2371–2379CrossRefGoogle Scholar
  68. 68.
    Wirth R, Chertkov O, Held B, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R et al (2011) Complete genome sequence of Desulfurococcus mucosus type strain (O7/1). Stand Genomic Sci 4:173–182CrossRefGoogle Scholar
  69. 69.
    Anderson I, Wirth R, Lucas S, Copeland A, Lapidus A, Cheng JF, Goodwin L, Pitluck S, Davenport K, Detter JC et al (2011) Complete genome sequence of Staphylothermus hellenicus P8. Stand Genomic Sci 5:12–20CrossRefGoogle Scholar
  70. 70.
    Mavromatis K, Sikorski J, Lapidus A, Glavina Del Rio T, Copeland A, Tice H, Cheng J-F, Lucas S, Chen F, Nolan M et al. (2010) Complete genome sequence of Alicyclobacillus acidocaldarius type strain (104-IA). Stand Genomic Sci 2:9–18Google Scholar

Copyright information

© Springer International Publishing Switzerland 2016

Authors and Affiliations

  • Sanjeev Dahal
    • 1
    • 2
    • 3
    Email author
  • Suresh Poudel
    • 1
    • 2
    • 3
  • R. Adam Thompson
    • 3
    • 4
  1. 1.UT-ORNL Graduate School of Genome Science and TechnologyUniversity of TennesseeKnoxvilleUSA
  2. 2.Oak Ridge National LaboratoryOak RidgeUSA
  3. 3.BioEnergy Science CenterOak Ridge National LaboratoryOak RidgeUSA
  4. 4.Bredesen Center for Interdisciplinary Research and Graduate EducationUniversity of TennesseeKnoxvilleUSA

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