Advertisement

Archives of Microbiology

, Volume 198, Issue 2, pp 115–127 | Cite as

Insights from genome of Clostridium butyricum INCQS635 reveal mechanisms to convert complex sugars for biofuel production

  • Thiago Bruce
  • Fernanda Gomes Leite
  • Milene Miranda
  • Cristiane C. Thompson
  • Nei PereiraJr.
  • Mariana Faber
  • Fabiano L. Thompson
Original Paper

Abstract

Clostridium butyricum is widely used to produce organic solvents such as ethanol, butanol and acetone. We sequenced the entire genome of C. butyricum INCQS635 by using Ion Torrent technology. We found a high contribution of sequences assigned for carbohydrate subsystems (15–20 % of known sequences). Annotation based on protein-conserved domains revealed a higher diversity of glycoside hydrolases than previously found in C. acetobutylicum ATCC824 strain. More than 30 glycoside hydrolases (GH) families were found; families of GH involved in degradation of galactan, cellulose, starch and chitin were identified as most abundant (close to 50 % of all sequences assigned as GH) in C. butyricum INCQS635. KEGG metabolic pathways reconstruction allowed us to verify possible routes in the C. butyricum INCQS635 and C. acetobutylicum ATCC824 genomes. Metabolic pathways for ethanol synthesis are similar for both species, but alcohol dehydrogenase of C. butyricum INCQS635 and C. acetobutylicum ATCC824 was different. The genomic repertoire of C. butyricum is an important resource to underpin future studies towards improved solvents production.

Keywords

Genomics Carbohydrate-active enzymes Biofuel Clostridium butyricum Ion Torrent 

Notes

Acknowledgments

The authors thank CNPq, CAPES and FAPERJ.

Supplementary material

203_2015_1166_MOESM1_ESM.png (139 kb)
Supplementary material 1 Number of sequences assigned by subsystems technology for each genome (PNG 138 kb)
203_2015_1166_MOESM2_ESM.png (32 kb)
Supplementary material 2 List of sequences assigned as enzymes involved in acetone synthesis in the tree fermentative Clostridium lineages. Table shows a description for each found in the sequenced genomes which were classified based on the EC number and functional role (PNG 32 kb)
203_2015_1166_MOESM3_ESM.png (303 kb)
Supplementary material 3 List of sequences assigned as enzymes compromised with butanol synthesis in the tree fermentative Clostridium lineages. Table presents the description for each found in the sequenced genomes which were classified based on EC number and functional role (PNG 303 kb)
203_2015_1166_MOESM4_ESM.png (90 kb)
Supplementary material 4 Homology between key enzymes for butanol synthesis in C. butyricum INCQS635 and C. acetobutylicum ATCC824 (PNG 89 kb)
203_2015_1166_MOESM5_ESM.png (48 kb)
Supplementary material 5 List of sequences assigned as enzymes compromised with ethanol synthesis in the tree fermentative Clostridium lineages. Table shows the description for each found in the sequenced genomes which were classified based on the EC number and functional role (PNG 48 kb)

References

  1. Aoki-Kinoshita K, Kanehisa M (2007) Gene annotation and pathway mapping in KEGG. In: Bergman N (ed) Comparative genomics. Humana Press, New York City, pp 71–91Google Scholar
  2. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M et al (2008) The RAST Server: rapid annotations using subsystems technology. BMC Genom 9:75CrossRefGoogle Scholar
  3. Braithwaite KL, Barna T, Spurway TD, Charnock SJ, Black GW, Hughes N, Lakey JH, Virden R, Hazlewood GP, Henrissat B et al (1997) Evidence that galactanase A from pseudomonas fluorescens subspecies cellulosa Is a retaining family 53 glycosyl hydrolase in which E161 and E270 are the catalytic residues. Biochemistry 36:15489–15500CrossRefPubMedGoogle Scholar
  4. Cai G, Jin B, Saint C, Monis P (2010) Metabolic flux analysis of hydrogen production network by Clostridium butyricum W5: effect of pH and glucose concentrations. Int J Hydrog Energy 35:6681–6690CrossRefGoogle Scholar
  5. Cai G, Jin B, Saint C, Monis P (2011) Genetic manipulation of butyrate formation pathways in Clostridium butyricum. J Biotechnol 155:269–274CrossRefPubMedGoogle Scholar
  6. Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V, Henrissat B (2009) The Carbohydrate-Active EnZymes database (CAZy): an expert resource for glycogenomics. Nucl Acids Res 37:D233–D238PubMedCentralCrossRefPubMedGoogle Scholar
  7. Chatzifragkou A, Aggelis G, Komaitis M, Zeng A-P, Papanikolaou S (2011) Impact of anaerobiosis strategy and bioreactor geometry on the biochemical response of Clostridium butyricum VPI 1718 during 1,3-propanediol fermentation. Bioresour Technol 102:10625–10632CrossRefPubMedGoogle Scholar
  8. Cheng C-L, Che P-Y, Chen B-Y, Lee W-J, Lin C-Y, Chang J-S (2012) Biobutanol production from agricultural waste by an acclimated mixed bacterial microflora. Appl Energy 100:3–9CrossRefGoogle Scholar
  9. Chevreux B, Pfisterer T, Drescher B, Driesel AJ, Müller WEG, Wetter T, Suhai S (2004) Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs. Genome Res 14:1147–1159PubMedCentralCrossRefPubMedGoogle Scholar
  10. Cho JK, Kim SY, Lee DH, Kim B, Jung JW (2012) Method for producing biofuel using marine algae-derived galactan. Google PatentsGoogle Scholar
  11. Cho JK, Kim SY, Lee DH, Kim B, Jung JW (2014) Method for producing biofuel using marine algae-derived galactan. Google PatentsGoogle Scholar
  12. Delattre C, Fenoradosoa TA, Michaud P (2011) Galactans: an overview of their most important sourcing and applications as natural polysaccharides. Braz Arch Biol Technol 54:1075–1092Google Scholar
  13. Dürre P (1998) New insights and novel developments in clostridial acetone/butanol/isopropanol fermentation. Appl Microbiol Biotechnol 49:639–648CrossRefGoogle Scholar
  14. Dvortsov IA, Lunina NA, Chekanovskaya LA, Schwarz WH, Zverlov VV, Velikodvorskaya GA (2009) Carbohydrate-binding properties of a separately folding protein module from β-1,3-glucanase Lic16A of Clostridium thermocellum. Microbiology 155:2442–2449CrossRefPubMedGoogle Scholar
  15. Eijsink VGH, Vaaje-Kolstad G, Vårum KM, Horn SJ (2008) Towards new enzymes for biofuels: lessons from chitinase research. Trends Biotechnol 26:228–235CrossRefPubMedGoogle Scholar
  16. FitzPatrick M, Champagne P, Cunningham MF, Whitney RA (2010) A biorefinery processing perspective: treatment of lignocellulosic materials for the production of value-added products. Bioresour Technol 101:8915–8922CrossRefPubMedGoogle Scholar
  17. Gheshlaghi R, Scharer JM, Moo-Young M, Chou CP (2009) Metabolic pathways of clostridia for producing butanol. Biotechnol Adv 27:764–781CrossRefPubMedGoogle Scholar
  18. González-Pajuelo M, Meynial-Salles I, Mendes F, Andrade JC, Vasconcelos I, Soucaille P (2005) Metabolic engineering of Clostridium acetobutylicum for the industrial production of 1,3-propanediol from glycerol. Metab Eng 7:329–336CrossRefPubMedGoogle Scholar
  19. Hallenbeck PC (2009) Fermentative hydrogen production: principles, progress, and prognosis. Int J Hydrogen Energy 34:7379–7389CrossRefGoogle Scholar
  20. Hinz SWA, Pastink MI, van den Broek LAM, Vincken J-P, Voragen AGJ (2005) Bifidobacterium longum Endogalactanase Liberates Galactotriose from Type I Galactans. Appl Environ Microbiol 71:5501–5510PubMedCentralCrossRefPubMedGoogle Scholar
  21. Hou X, Peng W, Xiong L, Huang C, Chen X, Chen X, Zhang W (2013) Engineering Clostridium acetobutylicum for alcohol production. J Biotechnol 166:25–33CrossRefPubMedGoogle Scholar
  22. Jang Y-S, Malaviya A, Cho C, Lee J, Lee SY (2012) Butanol production from renewable biomass by clostridia. Bioresour Technol 123:653–663CrossRefPubMedGoogle Scholar
  23. Jones DT, Woods DR (1986) Acetone-butanol fermentation revisited. Microbiol Rev 50:484–524PubMedCentralPubMedGoogle Scholar
  24. Koppová I, Bureš M, Šimůnek J (2012) Intestinal bacterial population of healthy rats during the administration of chitosan and chitooligosaccharides. Folia Microbiol 57:295–299CrossRefGoogle Scholar
  25. Kramhøft B, Bak-Jensen KS, Mori H, Juge N, Nøhr J, Svensson B (2005) Involvement of individual subsites and secondary substrate binding sites in multiple attack on amylose by barley α-amylase. Biochemistry 44:1824–1832CrossRefPubMedGoogle Scholar
  26. Kumar N, Ghosh A, Das D (2001) Redirection of biochemical pathways for the enhancement of H2 production by Enterobacter cloacae. Biotechnol Lett 23:537–541CrossRefGoogle Scholar
  27. Kumar R, Singh S, Singh O (2008) Bioconversion of lignocellulosic biomass: biochemical and molecular perspectives. J Ind Microbiol Biotechnol 35:377–391CrossRefPubMedGoogle Scholar
  28. Le Nours J, De Maria L, Welner D, Jørgensen CT, Christensen LLH, Borchert TV, Larsen S, Lo Leggio L (2009) Investigating the binding of β-1,4-galactan to Bacillus licheniformis β-1,4-galactanase by crystallography and computational modeling. Proteins Struct Funct Bioinform 75:977–989CrossRefGoogle Scholar
  29. Lee SY, Park JH, Jang SH, Nielsen LK, Kim J, Jung KS (2008) Fermentative butanol production by clostridia. Biotechnol Bioeng 101:209–228CrossRefPubMedGoogle Scholar
  30. Lee J, Jang Y-S, Choi SJ, Im JA, Song H, Cho JH, Seung DY, Papoutsakis ET, Bennett GN, Lee SY (2012) Metabolic Engineering of Clostridium acetobutylicum ATCC 824 for isopropanol-butanol-ethanol fermentation. Appl Environ Microbiol 78:1416–1423PubMedCentralCrossRefPubMedGoogle Scholar
  31. Li J, Baral N, Jha A (2014) Acetone–butanol–ethanol fermentation of corn stover by Clostridium species: present status and future perspectives. World J Microbiol Biotechnol 30:1145–1157CrossRefPubMedGoogle Scholar
  32. Lütke-Eversloh T, Bahl H (2011) Metabolic engineering of Clostridium acetobutylicum: recent advances to improve butanol production. Curr Opin Biotechnol 22:634–647CrossRefPubMedGoogle Scholar
  33. Lynd LR, Weimer PJ, van Zyl WH, Pretorius IS (2002) Microbial cellulose utilization: fundamentals and biotechnology. Microbiol Mol Biol Rev 66:506–577PubMedCentralCrossRefPubMedGoogle Scholar
  34. Lynd LR, Laser MS, Bransby D, Dale BE, Davison B, Hamilton R, Himmel M, Keller M, McMillan JD, Sheehan J et al (2008) How biotech can transform biofuels. Nat Biotech 26:169–172CrossRefGoogle Scholar
  35. Nölling J, Breton G, Omelchenko MV, Makarova KS, Zeng Q, Gibson R, Lee HM, Dubois J, Qiu D, Hitti J et al (2001) Genome sequence and comparative analysis of the solvent-producing bacterium Clostridium acetobutylicum. J Bacteriol 183:4823–4838PubMedCentralCrossRefPubMedGoogle Scholar
  36. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, Edwards RA, Gerdes S, Parrello B, Shukla M et al (2014) The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res 42:D206–D214PubMedCentralCrossRefPubMedGoogle Scholar
  37. Pagani I, Liolios K, Jansson J, Chen I-MA, Smirnova T, Nosrat B, Markowitz VM, Kyrpides NC (2012) The Genomes OnLine Database (GOLD) v. 4: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 40:D571–D579PubMedCentralCrossRefPubMedGoogle Scholar
  38. Park BH, Karpinets TV, Syed MH, Leuze MR, Uberbacher EC (2010) CAZymes Analysis Toolkit (CAT): web service for searching and analyzing carbohydrate-active enzymes in a newly sequenced organism using CAZy database. Glycobiology 20:1574–1584CrossRefPubMedGoogle Scholar
  39. Paulova L, Patakova P, Branska B, Rychtera M, Melzoch K (2015) Lignocellulosic ethanol: technology design and its impact on process efficiency. Biotechnol Adv 33(6 Pt 2):1091–1107. doi: 10.1016/j.biotechadv.2014.12.002 CrossRefPubMedGoogle Scholar
  40. Pitcher DG, Saunders NA, Owen RJ (1989) Rapid extraction of bacterial genomic DNA with guanidium thiocyanate. Lett Appl Microbiol 8:151–156CrossRefGoogle Scholar
  41. Quail MA, Smith M, Coupland P, Otto TD, Harris SR, Connor TR, Bertoni A, Swerdlow HP, Gu Y (2012) A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics 13:341PubMedCentralCrossRefPubMedGoogle Scholar
  42. Raynaud C, Sarçabal P, Meynial-Salles I, Croux C, Soucaille P (2003) Molecular characterization of the 1,3-propanediol (1,3-PD) operon of Clostridium butyricum. Proc Natl Acad Sci 100:5010–5015PubMedCentralCrossRefPubMedGoogle Scholar
  43. Raynaud C, Lee J, Sarçabal P, Croux C, Meynial-Salles I, Soucaille P (2011) Molecular characterization of the glycerol-oxidative pathway of Clostridium butyricum VPI 1718. J Bacteriol 193:3127–3134PubMedCentralCrossRefPubMedGoogle Scholar
  44. Sabathé F, Croux C, Cornillot E, Soucaille P (2002) amyP, a reporter gene to study strain degeneration in Clostridium acetobutylicum ATCC 824. FEMS Microbiol Lett 210:93–98CrossRefPubMedGoogle Scholar
  45. Saint-Amans S, Girbal L, Andrade J, Ahrens K, Soucaille P (2001) Regulation of carbon and electron Flow in Clostridium butyricum VPI 3266 grown on glucose-glycerol mixtures. J Bacteriol 183:1748–1754PubMedCentralCrossRefPubMedGoogle Scholar
  46. Sanderson K (2011) Lignocellulose: a chewy problem. Nature 474:S12–S14CrossRefPubMedGoogle Scholar
  47. Šimůnek J, Koppová I, Tiščenko G, Dohnálek J, Dušková J (2012) Excretome of the chitinolytic bacterium Clostridium paraputrificum J4. Folia Microbiol 57:335–339CrossRefGoogle Scholar
  48. Tummala SB, Junne SG, Papoutsakis ET (2003) Antisense RNA downregulation of coenzyme A transferase combined with alcohol-aldehyde dehydrogenase overexpression leads to predominantly alcohologenic Clostridium acetobutylicum fermentations. J Bacteriol 185:3644–3653PubMedCentralCrossRefPubMedGoogle Scholar
  49. Vernazza CL, Gibson GR, Rastall RA (2005) In vitro fermentation of chitosan derivatives by mixed cultures of human faecal bacteria. Carbohydr Polym 60:539–545CrossRefGoogle Scholar
  50. Wilson DB (2009) Cellulases and biofuels. Curr Opin Biotechnol 20:295–299CrossRefPubMedGoogle Scholar
  51. Xin B, Tao F, Wang Y, Gao C, Ma C, Xu P (2013) Genome sequence of Clostridium butyricum strain DSM 10702, a promising producer of biofuels and biochemicals. Genome Announc 1(4):e00563–13. doi: 10.1128/genomeA.00563-13 PubMedCentralCrossRefPubMedGoogle Scholar
  52. Zeng AP, Ross A, Biebl H, Tag C, Günzel B, Deckwer WD (1994) Multiple product inhibition and growth modeling of Clostridium butyricum and klebsiella pneumoniae in glycerol fermentation. Biotechnol Bioeng 44:902–911CrossRefPubMedGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2015

Authors and Affiliations

  • Thiago Bruce
    • 1
    • 4
  • Fernanda Gomes Leite
    • 1
  • Milene Miranda
    • 2
  • Cristiane C. Thompson
    • 2
  • Nei PereiraJr.
    • 3
  • Mariana Faber
    • 3
  • Fabiano L. Thompson
    • 2
  1. 1.Faculdade de Tecnologia e CiênciasLaboratory of Environmental BiotechnologySalvadorBrazil
  2. 2.Laboratory of Microbiology and SAGE-COPPEFederal University of Rio de Janeiro (UFRJ)Rio de JaneiroBrazil
  3. 3.Laboratory of Bioprocesses DevelopmentFederal University of Rio de Janeiro (UFRJ)Rio de JaneiroBrazil
  4. 4.Department of BiotechnologyFederal University of BahiaSalvadorBrazil

Personalised recommendations