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From genome sequence to integrated bioprocess for succinic acid production by Mannheimia succiniciproducens

Abstract

Mannheimia succiniciproducens is a capnophilic gram-negative bacterium isolated from bovine rumen. Wild-type M. succiniciproducens can produce succinic acid as a major fermentation product with acetic, formic, and lactic acids as byproducts during the anaerobic cultivation using several different carbon sources. Succinic acid is an important C4 building block chemical for many applications. Here, we review the progress made with M. succiniciproducens for efficient succinic acid production; the approaches taken towards the development of an integrated process for succinic acid production are described, which include strain isolation and characterization, complete genome sequencing and annotation, development of genetic tools for metabolic engineering, strain development by systems approach of integrating omics and in silico metabolic analysis, and development of fermentation and recovery processes. We also describe our current effort on further improving the performance of M. succiniciproducens and optimizing the mid- and downstream processes. Finally, we finish this mini-review by discussing the issues that need to be addressed to make this process of fermentative succinic acid production employing M. succiniciproducens to reach the industrial-scale process.

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References

  1. Bagos PG, Liakopoulos TD, Spyropoulos IC, Hamodrakas SJ (2004) PRED-TMBB: a web server for predicting the topology of beta-barrel outer membrane proteins. Nucleic Acids Res 32:W400–W404

  2. Barrett CL, Kim TY, Kim HU, Palsson BO, Lee SY (2006) Systems biology as a foundation for genome-scale synthetic biology. Curr Opin Biotechnol 17:488–492

  3. Becker SA, Palsson BO (2005) Genome-scale reconstruction of the metabolic network in Staphylococcus aureus N315: an initial draft to the two-dimensional annotation. BMC Microbiol 5:8

  4. Bendtsen JD, Nielsen H, von Heijne G, Brunak S (2004) Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 340:783–795

  5. Blomfield IC, Vaughn V, Rest RF, Eisenstein BI (1991) Allelic exchange in Escherichia coli using the Bacillus subtilis sacB gene and a temperature-sensitive pSC101 replicon. Mol Microbiol 5:1447–1457

  6. Borodina I, Krabben P, Nielsen J (2005) Genome-scale analysis of Streptomyces coelicolor A3(2) metabolism. Genome Res 15:820–829

  7. Datta R (1992) Process for the production of succinic acid by anaerobic fermentation. US Patent 5,143,833

  8. Datta R, Glassner DA, Jain MK, Vick Roy JR (1992) Fermentation and purification process for succinic acid. US Patent 5,168,055

  9. Datta R, Tsai SP, Bonsignore P, Moon SH, Frank JR (1995) Technological and economic potential of poly(lactic acid) and lactic acid derivatives. FEMS Microbiol Rev 16:221–231

  10. Duarte NC, Herrgard MJ, Palsson BO (2004) Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model. Genome Res 14:1298–1309

  11. Duarte NC, Becker SA, Jamshidi N, Thiele I, Mo ML, Vo TD, Srivas R, Palsson BO (2007) Global reconstruction of the human metabolic network based on genomic and bibliomic data. Proc Natl Acad Sci U S A 104:1777–1782

  12. Edwards JS, Palsson BO (1999) Systems properties of the Haemophilus influenzae Rd metabolic genotype. J Biol Chem 274:17410–17416

  13. Feist AM, Scholten JC, Palsson BO, Brockman FJ, Ideker T (2006) Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri. Mol Syst Biol 2:2006 0004

  14. Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO (2007) A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Mol Syst Biol 3:121

  15. Forster J, Famili I, Fu P, Palsson BO, Nielsen J (2003) Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Res 13:244–253

  16. Gardy JL, Laird MR, Chen F, Rey S, Walsh CJ, Ester M, Brinkman FS (2005) PSORTb v.2.0: expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis. Bioinformatics 21:617–623

  17. Glassner DA, Datta R (1992) Process for the production and purification of succinic acid. US Patent 5,143,834

  18. Guettler MV, Jain MK, Soni BK (1996a) Process for making succinic acid, microorganisms for use in the process and methods of obtaining the microorganisms. US Patent 5,504,004

  19. Guettler MV, Jain MK, Rumler D (1996b) Method for making succinic acid bacterial variants for use in the process, and method for obtaining variants. US Patent 5,573,931

  20. Guettler MV, Rumler D, Jain MK (1999) Actinobacillus succinogenes sp. nov., a novel succinic-acid-producing strain from the bovine rumen. Int J Syst Bacteriol 49(Pt 1):207–216

  21. Heinemann M, Kummel A, Ruinatscha R, Panke S (2005) In silico genome-scale reconstruction and validation of the Staphylococcus aureus metabolic network. Biotechnol Bioeng 92:850–864

  22. Hong SH, Lee SY (2000) Metabolic flux distribution in metabolically engineered Escherichia coli strain producing succinic acid. J Microbiol Biotechnol 10:496–501

  23. Hong SH, Lee SY (2001) Metabolic flux analysis for succinic acid production by recombinant Escherichia coli with amplified malic enzyme activity. Biotechnol Bioeng 74:89–95

  24. Hong YK, Hong WH (2005) Removal of acetic acid from aqueous solutions containing succinic acid and acetic acid by tri-n-octylamine. Sep Purif Technol 42:151–157

  25. Hong SH, Kim JS, Lee SY, In YH, Choi SS, Rih JK, Kim CH, Jeong H, Hur CG, Kim JJ (2004) The genome sequence of the capnophilic rumen bacterium Mannheimia succiniciproducens. Nat Biotechnol 22:1275–1281

  26. Huh YS, Hong YK, Hong WH, Chang HN (2004) Selective extraction of acetic acid from the fermentation broth produced by Mannheimia succiniciproducens. Biotechnol Lett 26:1581–1584

  27. Huh YS, Jun Y-S, Hong YK, Song H, Lee SY, Hong WH (2006) Effective purification of succinic acid from fermentation broth produced by Mannheimia succiniciproducens. Proc Biochem 41:1461–1465

  28. Hungate RE (1966) The rumen and its microbes. Academic, New York

  29. Jang YS, Jung YR, Lee SY, Kim JM, Lee JW, Oh DB, Kang HA, Kwon O, Jang SH, Song H, Lee SJ, Kang KY (2007) Construction and characterization of shuttle vectors for succinic acid-producing rumen bacteria. Appl Environ Microbiol 73:5411–5420

  30. Jun Y-S, Lee EZ, Huh YS, Hong YK, Hong WH, Lee SY (2007) Kinetic study for the extraction of succinic acid with TOA in fermentation broth: effects of pH, salt and contaminated acid. Biochem Eng J 36:8–13

  31. Kehrenberg C, Schwarz S (2002) Nucleotide sequence and organization of plasmid pMVSCS1 from Mannheimia varigena: identification of a multiresistance gene cluster. J Antimicrob Chemother 49:383–386

  32. Kim DY, Yim SC, Lee PC, Lee WG, Lee SY, Chang HN (2004) Batch and continuous fermentation of succinic acid from wood hydrolysate by Mannheimia succiniciproducens MBEL55E. Enzyme Microbial Technol 35:648–653

  33. Kim TY, Kim HU, Park JM, Song H, Kim JS, Lee SY (2007) Genome-scale analysis of Mannheimia succiniciproducens metabolism. Biotechnol Bioeng 97:657–671

  34. Kim HU, Kim TY, Lee SY (2008a) Metabolic flux analysis and metabolic engineering of microorganisms. Mol Biosyst 4:113–120

  35. Kim JM, Lee KH, Lee SY (2008b) Development of a markerless gene knock-out system for Mannheimia succiniciproducens using a temperature-sensitive plasmid. FEMS Microbiol Lett 278:78–85

  36. Lee PC, Lee WG, Kwon S, Lee SY, Chang HN (1999a) Succinic acid production by Anaerobiospirillum succiniciproducens: effects of the H2/CO2 supply and glucose concentration. Enzyme Microb Technol 24:559–554

  37. Lee PC, Lee WG, Lee SY, Chang HN (1999b) Effects of medium components on the growth of Anaerobiospirillum succiniciproducens and succinic acid production. Process Biochem 35:49–55

  38. Lee PC, Lee WG, Lee SY, Chang HN (2001) Succinic acid production with reduced by-product formation in the fermentation of Anaerobiospirillum succiniciproducens using glycerol as a carbon source. Biotechnol Bioeng 72:41–48

  39. Lee PC, Lee SY, Hong SH, Chang HN (2002a) Isolation and characterization of a new succinic acid-producing bacterium, Mannheimia succiniciproducens MBEL55E, from bovine rumen. Appl Microbiol Biotechnol 58:663–668

  40. Lee SY, Hong SH, Moon SY (2002b) In silico metabolic pathway analysis and design: succinic acid production by metabolically engineered Escherichia coli as an example. Genome Inform 13:214–223

  41. Lee PC, Lee SY, Hong SH, Chang HN (2003) Batch and continuous cultures of Mannheimia succiniciproducens MBEL55E for the production of succinic acid from whey and corn steep liquor. Bioprocess Biosyst Eng 26:63–67

  42. Lee SJ, Lee DY, Kim TY, Kim BH, Lee J, Lee SY (2005a) Metabolic engineering of Escherichia coli for enhanced production of succinic acid, based on genome comparison and in silico gene knockout simulation. Appl Environ Microbiol 71:7880–7887

  43. Lee SY, Lee D-Y, Kim TY (2005b) Systems biotechnology for strain improvement. Trends Biotechnol 23:349–358

  44. Lee SY, Woo HM, Lee D-Y, Choi HS, Kim TY, Yun H (2005c) Systems-level analysis of genome-scale microbial metabolism under the integrated software environment. Biotechnol Bioproc Eng 10:425–431

  45. Lee JW, Lee SY, Song H, Yoo JS (2006a) The proteome of Mannheimia succiniciproducens, a capnophilic rumen bacterium. Proteomics 6:3550–3566

  46. Lee SJ, Song H, Lee SY (2006b) Genome-based metabolic engineering of Mannheimia succiniciproducens for succinic acid production. Appl Environ Microbiol 72:1939–1948

  47. Lin H, Bennett GN, San KY (2005a) Fed-batch culture of a metabolically engineered Escherichia coli strain designed for high-level succinate production and yield under aerobic conditions. Biotechnol Bioeng 90:775–779

  48. Lin H, Bennett GN, San KY (2005b) Metabolic engineering of aerobic succinate production systems in Escherichia coli to improve process productivity and achieve the maximum theoretical succinate yield. Metab Eng 7:116–127

  49. McKinlay JB, Vieille C, Zeikus G (2007) Prospects for a bio-based succinate industry. Appl Microbiol Biotechnol 76:727–740

  50. Oliveira AP, Nielsen J, Forster J (2005) Modeling Lactococcus lactis using a genome-scale flux model. BMC Microbiol 5:39

  51. Qin M, Bayley C, Stockton T, Ow DW (1994) Cre recombinase-mediated site-specific recombination between plant chromosomes. Proc Natl Acad Sci U S A 91:1706–1710

  52. Price ND, Reed JL, Palsson BO (2004) Genome-scale models of microbial cells: evaluating the consequences of constraints. Nat Rev Microbiol 2:886–897

  53. Reed JL, Vo TD, Schilling CH, Palsson BO (2003) An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). Genome Biol 4:R54

  54. Schilling CH, Covert MW, Famili I, Church GM, Edwards JS, Palsson BO (2002) Genome-scale metabolic model of Helicobacter pylori 26695. J Bacteriol 184:4582–4593

  55. Song H, Lee SY (2006) Production of succinic acid by bacterial fermentation. Enzyme Microb. Technol 39:352–361

  56. Song H, Huh YS, Lee SY, Hong WH, Hong YK (2007a) Recovery of succinic acid produced by fermentation of a metabolically engineered Mannheimia succiniciproducens strain. J Biotechnol 132:445–452

  57. Song H, Lee JW, Choi S, You JK, Hong WH, Lee SY (2007b) Effects of dissolved CO2 levels on the growth of Mannheimia succiniciproducens and succinic acid production. Biotechnol Bioeng 98:1296–1304

  58. Suzuki N, Nonaka H, Tsuge Y, Inui M, Yukawa H (2005) New multiple-deletion method for the Corynebacterium glutamicum genome, using a mutant lox sequence. Appl Environ Microbiol 71:8472–8480

  59. Teusink B, van Enckevort FH, Francke C, Wiersma A, Wegkamp A, Smid EJ, Siezen RJ (2005) In silico reconstruction of the metabolic pathways of Lactobacillus plantarum: comparing predictions of nutrient requirements with those from growth experiments. Appl Environ Microbiol 71:7253–7262

  60. Thiele I, Vo TD, Price ND, Palsson BO (2005) Expanded metabolic reconstruction of Helicobacter pylori (iIT341 GSM/GPR): an in silico genome-scale characterization of single- and double-deletion mutants. J Bacteriol 187:5818–5830

  61. Urbance SE, Pometto AL 3rd, Dispirito AA, Denli Y (2004) Evaluation of succinic acid continuous and repeat-batch biofilm fermentation by Actinobacillus succinogenes using plastic composite support bioreactors. Appl Microbiol Biotechnol 65:664–670

  62. Van Deursen J, Fornerod M, Van Rees B, Grosveld G (1995) Cre-mediated site-specific translocation between nonhomologous mouse chromosomes. Proc Natl Acad Sci U S A 92:7376–7380

  63. van der Werf MJ, Guettler MV, Jain MK, Zeikus JG (1997) Environmental and physiological factors affecting the succinate product ratio during carbohydrate fermentation by Actinobacillus sp. 130Z. Arch Microbiol 167:332–342

  64. Vemuri GN, Eiteman MA, Altman E (2002) Succinate production in dual-phase Escherichia coli fermentations depends on the time of transition from aerobic to anaerobic conditions. J Ind Microbiol Biotechnol 28:325–332

  65. Willke T, Vorlop KD (2004) Industrial bioconversion of renewable resources as an alternative to conventional chemistry. Appl Microbiol Biotechnol 66:131–142

  66. Yedur S, Berglund KA, Dunuwila DD (2001) Succinic acid production and purification. US Patent 6,265,190 B1

  67. Zeikus JG, Jain MK, Elankovan P (1999) Biotechnology of succinic acid production and markets for derived industrial products. Appl Microbiol Biotechnol 51:545–552

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Acknowledgments

This work was supported by the Genome-based Integrated Bioprocess Project of the Ministry of Science and Technology. Further supports by the LG Chem Chair Professorship, IBM SUR program, and Microsoft are appreciated.

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Correspondence to Sang Yup Lee.

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Lee, S.Y., Kim, J.M., Song, H. et al. From genome sequence to integrated bioprocess for succinic acid production by Mannheimia succiniciproducens . Appl Microbiol Biotechnol 79, 11–22 (2008). https://doi.org/10.1007/s00253-008-1424-3

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Keywords

  • Mannheimia succiniciproducens
  • Genome
  • Succinic acid
  • Metabolic engineering
  • Fermentation
  • Recovery