Skip to main content
SpringerLink
Log in

Genomics on Pretreatment Inhibitor Tolerance of Zymomonas mobilis

  • Chapter
  • First Online:
Microbial Stress Tolerance for Biofuels

Part of the book series: Microbiology Monographs ((MICROMONO,volume 22))

Abstract

The development and use of robust ethanologenic microorganisms resistant to industrially relevant pretreatment inhibitors will be a critical component in the successful generation of biofuel on the industrial scale. Recent progress to understand the genetic basis of pretreatment inhibitor tolerance using genomics and systems biology tools for metabolic engineering for the model ethanologenic bacterium Zymomonas mobilis is reviewed in this chapter. The importance of accurate genome annotations and the integration of systems biology data for annotation improvement are highlighted, and case studies that describe the identification and characterization of the Z. mobilis nhaA, hfq, and himA inhibitor tolerance related gene targets are presented.

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 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
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

References

  • Almeida JRM, Modig T, Petersson A, Hahn-Hagerdal B, Liden G, Gorwa-Grauslund MF (2007) Increased tolerance and conversion of inhibitors in lignocellulosic hydrolysates by Saccharomyces cerevisiae. J Chem Technol Biotechnol 82:340–349

    Article  CAS  Google Scholar 

  • Alper H, Stephanopoulos G (2007) Global transcription machinery engineering: a new approach for improving cellular phenotype. Metab Eng 9:258–267

    Article  PubMed  CAS  Google Scholar 

  • Alper H, Stephanopoulos G (2009) Engineering for biofuels: exploiting innate microbial capacity or importing biosynthetic potential? Nat Rev Micro 7:715–723

    Article  CAS  Google Scholar 

  • Alper H, Moxley J, Nevoigt E, Fink GR, Stephanopoulos G (2006) Engineering yeast transcription machinery for improved ethanol tolerance and production. Science 314:1565–1568

    Article  PubMed  CAS  Google Scholar 

  • Armengaud J (2009) A perfect genome annotation is within reach with the proteomics and genomics alliance. Curr Opin Microbiol 12:292–300

    Article  PubMed  CAS  Google Scholar 

  • Baudet M, Ortet P, Gaillard JC, Fernandez B, Guerin P, Enjalbal C, Subra G, de Groot A, Barakat M, Dedieu A, Armengaud J (2010) Proteomics-based refinement of Deinococcus deserti genome annotation reveals an unwanted use of non-canonical translation initiation codons. Mol Cell Proteomics 9:415–426

    Article  PubMed  CAS  Google Scholar 

  • Cho BK, Charusanti P, Herrgard MJ, Palsson BO (2007) Microbial regulatory and metabolic networks. Curr Opin Biotechnol 18:360–364

    Article  PubMed  CAS  Google Scholar 

  • Deanda K, Zhang M, Eddy C, Picataggio S (1996) Development of an arabinose-fermenting Zymomonas mobilis strain by metabolic pathway engineering. Appl Environ Microbiol 62:4465–4470

    PubMed  CAS  Google Scholar 

  • Devos D, Valencia A (2001) Intrinsic errors in genome annotation. Trends Genet 17:429–431

    Article  PubMed  CAS  Google Scholar 

  • Dien BS, Cotta MA, Jeffries TW (2003) Bacteria engineered for fuel ethanol production: current status. Applied Microbiol Biotechnol 63:258–266

    Article  CAS  Google Scholar 

  • Earl AM, Mohundro MM, Mian IS, Battista JR (2002) The IrrE protein of Deinococcus radiodurans R1 is a novel regulator of recA expression. J Bacteriol 184:6216–6224

    Article  PubMed  CAS  Google Scholar 

  • Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, Bult CJ, Tomb JF, Dougherty BA, Merrick JM et al (1995) Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269:496–512

    Article  PubMed  CAS  Google Scholar 

  • Gao GJ, Tian B, Liu LL, Sheng DH, Shen BH, Hua YJ (2003) Expression of Deinococcus radiodurans PprI enhances the radioresistance of Escherichia coli. DNA Repair 2:1419–1427

    Article  PubMed  CAS  Google Scholar 

  • Hahn-Hagerdal B, Galbe M, Gorwa-Grauslund MF, Liden G, Zacchi G (2006) Bio-ethanol–the fuel of tomorrow from the residues of today. Trends Biotechnol 24:549–556

    Article  PubMed  CAS  Google Scholar 

  • Himmel ME, Ding SY, Johnson DK, Adney WS, Nimlos MR, Brady JW, Foust TD (2007) Biomass recalcitrance: Engineering plants and enzymes for biofuels production. Science 315:804–807

    Article  PubMed  CAS  Google Scholar 

  • Jeffries TW (2005) Ethanol fermentation on the move. Nat Biotechnol 23(1):40–41

    Article  PubMed  CAS  Google Scholar 

  • Jeon YJ, Svenson CJ, Joachimsthal EL, Rogers PL (2002) Kinetic analysis of ethanol production by an acetate-resistant strain of recombinant Zymomonas mobilis. Biotechnol Lett 24:819–824

    Article  CAS  Google Scholar 

  • Joachimstahl E, Haggett KD, Jang JH, Rogers PL (1998) A mutant of Zymomonas mobilis ZM4 capable of ethanol production from glucose in the presence of high acetate concentrations. Biotechnol Lett 20:137–142

    Article  Google Scholar 

  • Kadar Z, Maltha SF, Szengyel Z, Reczey K, De Laat W (2007) Ethanol fermentation of various pretreated and hydrolyzed substrates at low initial pH. Appl Biochem Biotechnol 137:847–858

    Article  PubMed  Google Scholar 

  • Kerr AL, Jeon YJ, Svenson CJ, Rogers PL, Neilan BA (2010) DNA restriction-modification systems in the ethanologen, Zymomonas mobilis ZM4. Appl Microbiol Biotechnol 89:761–769

    Article  PubMed  Google Scholar 

  • Kim IS, Barrow KD, Rogers PL (2000) Nuclear magnetic resonance studies of acetic acid inhibition of rec Zymomonas mobilis ZM4(pZB5). Appl Biochem Biotechnol 84–6:357–370

    Article  Google Scholar 

  • Klinke HB, Thomsen AB, Ahring BK (2004) Inhibition of ethanol-producing yeast and bacteria by degradation products produced during pre-treatment of biomass. Appl Microbiol Biotechnol 66:10–26

    Article  PubMed  CAS  Google Scholar 

  • Kouvelis VN, Saunders E, Brettin TS, Bruce D, Detter C, Han C, Typas MA, Pappas KM (2009) Complete genome sequence of the ethanol producer Zymomonas mobilis NCIMB 11163. J Bacteriol 191:7140–7141

    Article  PubMed  CAS  Google Scholar 

  • Lawford HG, Rousseau JD (1993) The effect of acetic acid on fuel ethanol-Production by Zymomonas. Appl Biochem Biotechnol 39:687–699

    Article  Google Scholar 

  • Lawford HG, Rousseau JD (1998) Improving fermentation performance of recombinant Zymomonas in acetic acid-containing media. Appl Biochem Biotechnol 70–2:161–172

    Article  Google Scholar 

  • Lawford HG, Rousseau JD, Tolan JS (2001) Comparative ethanol productivities of different Zymomonas recombinants fermenting oat hull hydrolysate. Appl Biochem Biotechnol 91–3:133–146

    Article  Google Scholar 

  • Lee K, Park J, Kim T, Yun H, Lee S (2010) The genome-scale metabolic network analysis of Zymomonas mobilis ZM4 explains physiological features and suggests ethanol and succinic acid production strategies. Microb Cell Fact 9:94

    Article  PubMed  CAS  Google Scholar 

  • Linger JG, Adney WS, Darzins A (2010) Heterologous expression and extracellular secretion of cellulolytic enzymes by Zymomonas mobilis. Appl Environ Microbiol 76:6360–6369

    Article  PubMed  CAS  Google Scholar 

  • Liu Z, Blaschek H (2010) Biomass conversion inhibitors and in situ detoxification. In: Vertes A, Qureshi N, Yukawa H, Blaschek H (eds) Biomass to biofuels: strategies for global industries. Wiley, West Sussex, p 27

    Google Scholar 

  • Liu ZL, Moon J (2009) A novel NADPH-dependent aldehyde reductase gene from Saccharomyces cerevisiae NRRL Y-12632 involved in the detoxification of aldehyde inhibitors derived from lignocellulosic biomass conversion. Gene 446:1–10

    Article  PubMed  CAS  Google Scholar 

  • Liu ZL, Slininger PJ, Dien BS, Berhow MA, Kurtzman CP, Gorsich SW (2004) Adaptive response of yeasts to furfural and 5-hydroxymethylfurfural and new chemical evidence for HMF conversion to 2,5-bis-hydroxymethylfuran. J Ind Microbiol Biotechnol 31:345–352

    PubMed  CAS  Google Scholar 

  • Liu ZL, Slininger PJ, Gorsich SW (2005) Enhanced biotransformation of furfural and hydroxymethylfurfural by newly developed ethanologenic yeast strains. Appl Biochem Biotechnol 121–124:451–460

    Article  PubMed  Google Scholar 

  • Liu ZL, Moon J, Andersh BJ, Slininger PJ, Weber S (2008) Multiple gene-mediated NAD(P)H-dependent aldehyde reduction is a mechanism of in situ detoxification of furfural and 5-hydroxymethylfurfural by Saccharomyces cerevisiae. Applied Microbiol Biotechnol 81:743–753

    Article  CAS  Google Scholar 

  • Liu ZL, Ma M, Song M (2009) Evolutionarily engineered ethanologenic yeast detoxifies lignocellulosic biomass conversion inhibitors by reprogrammed pathways. Mol Genet Genomics 282:233–244

    Article  PubMed  Google Scholar 

  • MacLean D, Jones JD, Studholme DJ (2009) Application of ‘next-generation’ sequencing technologies to microbial genetics. Nat Rev 7:287–296

    Google Scholar 

  • McMillan JD (1994) Conversion of hemicellulose hydrolyzates to ethanol. In: Himmel ME, Baker JO, Overend RP (eds) Enzymatic conversion of biomass for fuels production, vol 566, ACS Symposium Series., pp 411–437

    Chapter  Google Scholar 

  • Metzker ML (2010) Sequencing technologies – the next generation. Nat Rev Genet 11:31–46

    Article  PubMed  CAS  Google Scholar 

  • Mills T, Sandoval N, Gill R (2009) Cellulosic hydrolysate toxicity and tolerance mechanisms in Escherichia coli. Biotechnol Biofuels 2:26

    Article  PubMed  Google Scholar 

  • Palmqvist E, Hahn-Hägerdal B (2000) Fermentation of lignocellulosic hydrolysates II: inhibitors and mechanisms of inhibition. Biores Technol 74:25–33

    Article  CAS  Google Scholar 

  • Pan J, Wang J, Zhou ZF, Yan YL, Zhang W, Lu W, Ping S, Dai QL, Yuan ML, Feng B, Hou XG, Zhang Y, Ma R, Liu T, Feng L, Wang L, Chen M, Lin M (2009) IrrE, a global regulator of extreme radiation resistance in Deinococcus radiodurans, enhances salt tolerance in Escherichia coli and Brassica napus. PLoS One 4:2

    Google Scholar 

  • Panesar PS, Marwaha SS, Kennedy JF (2006) Zymomonas mobilis: an alternative ethanol producer. J Chem Technol Biotechnol 81:623–635

    Article  CAS  Google Scholar 

  • Parekh S, Vinci VA, Strobel RJ (2000) Improvement of microbial strains and fermentation processes. Appl Microbiol Biotechnol 54:287–301

    Article  PubMed  CAS  Google Scholar 

  • Park JH, Lee SY, Kim TY, Kim HU (2008) Application of systems biology for bioprocess development. Trends Biotechnol 26:404–412

    Article  PubMed  CAS  Google Scholar 

  • Patnaik R (2008) Engineering complex phenotypes in industrial strains. Biotechnol Prog 24:38–47

    Article  PubMed  CAS  Google Scholar 

  • Payne SH, Huang ST, Pieper R (2010) A proteogenomic update to Yersinia: enhancing genome annotation. BMC Genomics 11:460

    PubMed  Google Scholar 

  • Pienkos PT, Zhang M (2010) Role of pretreatment and conditioning processes on toxicity of lignocellulosic biomass hydrolysates. Cellulose 16:20

    Google Scholar 

  • Ranatunga TD, Jervis J, Helm RF, McMillan JD, Hatzis C (1997) Identification of inhibitory components toxic toward Zymomonas mobilis CP4(pZB5) xylose fermentation. Appl Biochem Biotechnol 67:185–198

    Article  CAS  Google Scholar 

  • Rogers PL, Jeon YJ, Lee KJ, Lawford HG (2007) Zymomonas mobilis for fuel ethanol and higher value products. In: Biofuels, vol 108. Advances in Biochemical Engineering/ Biotechnology. pp 263–288

    Google Scholar 

  • Seo JS, Chong HY, Park HS, Yoon KO, Jung C, Kim JJ, Hong JH, Kim H, Kim JH, Kil JI, Park CJ, Oh HM, Lee JS, Jin SJ, Um HW, Lee HJ, Oh SJ, Kim JY, Kang HL, Lee SY, Lee KJ, Kang HS (2005) The genome sequence of the ethanologenic bacterium Zymomonas mobilis ZM4. Nat Biotechnol 23:63–68

    Article  PubMed  CAS  Google Scholar 

  • Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT, Hinton JC, Vogel J (2008) Deep sequencing analysis of small noncoding RNA and mRNA targets of the global post-transcriptional regulator. Hfq PLoS Genet 4:8

    Article  Google Scholar 

  • Stephanopoulos G (2007) Challenges in engineering microbes for biofuels production. Science 315:801–804

    Article  PubMed  CAS  Google Scholar 

  • Takahashi CM, Takahashi DF, Carvalhal MLC, Alterthum F (1999) Effects of acetate on the growth and fermentation performance of Escherichia coli KO11. Appl Biochem Biotechnol 81:193–203

    Article  PubMed  CAS  Google Scholar 

  • Tsui HC, Leung HC, Winkler ME (1994) Characterization of broadly pleiotropic phenotypes caused by an hfq insertion mutation in Escherichia coli K-12. Mol Microbiol 13:35–49

    Article  PubMed  CAS  Google Scholar 

  • Tyo KE, Alper HS, Stephanopoulos GN (2007) Expanding the metabolic engineering toolbox: more options to engineer cells. Trends Biotechnol 25:132–137

    Article  PubMed  CAS  Google Scholar 

  • Valentin-Hansen P, Eriksen M, Udesen C (2004) The bacterial Sm-like protein Hfq: a key player in RNA transactions. Mol Microbiol 51:1525–1533

    Article  PubMed  CAS  Google Scholar 

  • Viitanen PV, Tao L, Knoke K, Zhang Y, Caimi PG, Zhang M, Chou Y, Franden M (2009) Process for the production of ethanol from a medium comprising xylose, employing a recombinant Zymomonas strain having a reduced himA expression. Patent WO/2009/058938

    Google Scholar 

  • White O, Eisen JA, Heidelberg JF, Hickey EK, Peterson JD, Dodson RJ, Haft DH, Gwinn ML, Nelson WC, Richardson DL, Moffat KS, Qin H, Jiang L, Pamphile W, Crosby M, Shen M, Vamathevan JJ, Lam P, McDonald L, Utterback T, Zalewski C, Makarova KS, Aravind L, Daly MJ, Minton KW, Fleischmann RD, Ketchum KA, Nelson KE, Salzberg S, Smith HO, Venter JC, Fraser CM (1999) Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1. Science 286:1571–1577

    Article  PubMed  CAS  Google Scholar 

  • Widiastuti H, Kim JY, Selvarasu S, Karimi IA, Kim H, Seo JS, Lee DY (2010) Genome-scale modeling and in silico analysis of ethanologenic bacteria Zymomonas mobilis. Biotechnol Bioeng 108:655–665

    Article  PubMed  Google Scholar 

  • Wright JC, Sugden D, Francis-McIntyre S, Riba-Garcia I, Gaskell SJ, Grigoriev IV, Baker SE, Beynon RJ, Hubbard SJ (2009) Exploiting proteomic data for genome annotation and gene model validation in Aspergillus niger. BMC Genomics 10:61

    Article  PubMed  Google Scholar 

  • Yablonsky MD, Goodman AE, Stevnsborg N, Delima OG, Demorais JOF, Lawford HG, Rogers PL, Eveleigh DE (1988) Zymomonas mobilis CP4: a clarification of strains via plasmid profiles. J Biotechnol 9:71–79

    Article  Google Scholar 

  • Yang S, Pappas KM, Hauser LJ, Land ML, Chen G-L, Hurst GB, Pan C, Kouvelis V, Typas M, Pelletier DA, Klingeman DM, Chang Y-J, Samatova NF, Brown SD (2009a) Improved genome annotation for Zymomonas mobilis. Nat Biotechnol 27:893–894

    Article  PubMed  CAS  Google Scholar 

  • Yang S, Tschaplinski TJ, Engle NL, Carroll SL, Martin SL, Davison BH, Palumbo AV, Rodriguez M Jr, Brown SD (2009b) Transcriptomic and metabolomic profiling of Zymomonas mobilis during aerobic and anaerobic fermentations. BMC Genomics 10:34

    Article  PubMed  Google Scholar 

  • Yang S, Land ML, Klingeman DM, Pelletier DA, Lu T-YS, Martin SL, Guo HB, Smith JC, Brown SD (2010a) Paradigm for industrial strain improvement identifies sodium acetate tolerance loci in Zymomonas mobilis and Saccharomyces cerevisiae. Proc Natl Acad Sci USA 107:10395–10400

    Article  PubMed  CAS  Google Scholar 

  • Yang S, Pelletier DA, Lu TY, Brown SD (2010b) The Zymomonas mobilis regulator hfq contributes to tolerance against multiple lignocellulosic pretreatment inhibitors. BMC Microbiol 10:135

    Article  PubMed  Google Scholar 

  • Zhang M, Eddy C, Deanda K, Finkestein M, Picataggio S (1995) Metabolic engineering of a pentose metabolism pathway in ethanologenic Zymomonas mobilis. Science 267:240–243

    Article  PubMed  CAS  Google Scholar 

  • Zhang A, Wassarman KM, Rosenow C, Tjaden BC, Storz G, Gottesman S (2003) Global analysis of small RNA and mRNA targets of Hfq. Mol Microbiol 50:1111–1124

    Article  PubMed  CAS  Google Scholar 

  • Zhang Y, Ma RQ, Zhao ZL, Zhou ZF, Lu W, Zhang W, Chen M (2010) irrE, an exogenous gene from Deinococcus radiodurans, improves the growth of and ethanol production by a Zymomonas mobilis strain under ethanol and acid stresses. J Microbiol Biotechnol 20:1156–1162

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

The authors would like to thank Meghan M. Drake for her careful review and suggestions. The BioEnergy Science Center is a US Department of Energy Bioenergy Research Center supported by the Office of Biological and Environmental Research in the DOE Office of Science. This manuscript has been authored by UT-Battelle, LLC, under Contract No. DE-AC05-00OR22725 with the US Department of Energy.

Author information

Authors and Affiliations

  1. Biosciences Division and BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA

    Shihui Yang, Martin Keller & Steven D. Brown

Authors
  1. Shihui Yang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Martin Keller
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Steven D. Brown
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Steven D. Brown .

Editor information

Editors and Affiliations

  1. USDA-ARS, National Center for Agricultural Utiliza USDA-ARS, PEORIA, Illinois, USA

    Zonglin Lewis Liu

Rights and permissions

Reprints and permissions

Copyright information

© 2012 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Yang, S., Keller, M., Brown, S.D. (2012). Genomics on Pretreatment Inhibitor Tolerance of Zymomonas mobilis . In: Liu, Z. (eds) Microbial Stress Tolerance for Biofuels. Microbiology Monographs, vol 22. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-21467-7_7

Download citation

Publish with us

Policies and ethics

Search

Navigation