Skip to main content
SpringerLink
Log in

Genome-wide transcriptomic analysis of a flocculent strain of Zymomonas mobilis

  • Genomics, transcriptomics, proteomics
  • Published:
Applied Microbiology and Biotechnology Aims and scope Submit manuscript

Abstract

ZM401, a flocculent mutant strain of Zymomonas mobilis ZM4 was studied using genome-wide transcriptomic analysis for evidence related to phenotypic changes associated with its cell–cell attachment behaviour. Batch fermentation studies with ZM401 and its parent strain ZM4 demonstrated that similar ethanol yields and productivities could be achieved with both strains indicating the potential of the flocculent strains for cost-effective cell biomass recycling with resultant high ethanol volumetric productivities. The results showed that twofold or greater differential expression occurred for 26 genes of ZM401 when compared to those of ZM4. Among these, significant over-expression was evident for the genes ZMO1083 and ZMO1084 which are associated with bacterial cellulose synthesis, while reduced expression was found for ZMO0614, ZMO0613, and ZMO0635 which are all associated with synthesis of flagella-related proteins. Both enhanced cellulose production and reduced flagella activity are likely to facilitate more stable flocculent behaviour in ZM401. From comparative DNA sequence analysis of these 26 genes, only one single point mutation was identified. This occurred at the amino acid position A525V of ZMO1055 which encodes for diguanyl cyclase/phosphoesterase which may be related to cell motility and cellulose synthesis in Z. mobilis.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

References

  • Chan C, Paul R, Samoray D, Amiot NC, Giese B, Jenal U, Schirmer T (2004) Structural basis of activity and allosteric control of diguanylate cyclase. Proc Natl Acad Sci 101(49):17084–17089

    Article  CAS  Google Scholar 

  • Christen B, Christen M, Paul R, Schmid F, Folcher M, Jenoe P, Meuwly M, Jenal U (2006) Allosteric control of cyclic di-GMP signalling. J Biol Chem 281:32015–32024

    Article  CAS  Google Scholar 

  • Cleveland WS, Devlin SJ (1988) Locally-weighted regression: an approach to regression analysis by local fitting. J Am Stat Assoc 83(403):596–610

    Article  Google Scholar 

  • Cui X, Churchill GA (2003) Genome Biol 4(4):210–215

    Google Scholar 

  • D'Argenio DA, Miller SI (2004) Cyclic di-GMP as a bacterial second messenger. Microbiology 150(8):2497–2502

    Article  Google Scholar 

  • Goodman AE, Rogers PL, Skotnicki ML (1982) Minimal medium for isolation of auxotrophic Zymomonas mutants. Appl Environ Microbiol 44(2):496–498

    CAS  Google Scholar 

  • Hughes J, Ramsden DK, Boulby JM (1994) The role of cellulosics in chitosan flocculation of Zymomonas mobilis. Biotechnol Lett 8:541–546

    CAS  Google Scholar 

  • Jared EF, Lawford GR, Bogdan CZ, Robert CC (1983) High productivity continuous ethanol fermentation with a flocculating mutant strain of Zymomonas mobilis. Biotechnol Lett 5(1):19–24

    Google Scholar 

  • Jenal U, Malone J (2006) Mechanisms of cyclic-di-GMP signalling in bacteria. Ann Rev Genet 40:385–407

    Article  CAS  Google Scholar 

  • Kadota K, Miki R, Bono H, Shimizu K, Okazaki Y, Hayashizaki Y (2001) Preprocessing implementation for microarray (PRIM): an efficient method for processing cDNA microarray data. Physiol Genom 4(3):183–188

    CAS  Google Scholar 

  • Kerr AL, Jeon YJ, Svenson CJ, Rogers PL, Neilan BA (2011) DNA restriction-modification systems in the ethanologen, Zymomonas mobilis ZM4. Appl Microbiol Biotechnol 89(3):761–769

    Article  CAS  Google Scholar 

  • Lau MW, Gunawan C, Balan V, Dale BE (2010) Comparing the fermentation performance of Escherichia coli KO11, Saccharomyces cerevisiae 424A(LNH-ST) and Zymomonas mobilis AX101 for cellulosic ethanol production. Biotechnol Biofuels 3:11

    Article  Google Scholar 

  • Lee JH, Skotnicki ML, Rogers PL (1982) Kinetic studies on a flocculent strain of Zymomonas mobilis. Biotechnol Lett 4:615–620

    Article  CAS  Google Scholar 

  • Lee KY, Park JM, Kim TY, Yun HS, Lee SY (2010) The genome-scale metabolic network analysis of Zymomonas mobilis ZM4 explains physiological features and suggests ethanol and succinic acid production strategies. Microbiol Cell Factories. doi:10.1186/1475-2859-9-94

  • Linger JG, Adney WS, Darzins A (2010) Heterologous expression and extracellular secretion of cellulolytic enzymes in Zymomonas mobilis. Appl Environ Microbiol 76(19):6360–6369

    Article  CAS  Google Scholar 

  • Rogers PL, Jeon YJ, Lee KJ, Lawford HG (2007) Zymomonas mobilis for fuel ethanol and higher value products. Adv Biochem Eng Biotechnol 108:263–288

    CAS  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  CAS  Google Scholar 

  • Skotnicki ML, Warr RG, Goodman AE, Lee KJ, Rogers PL (1984) High-productivity alcohol fermentation using Zymomonas mobilis. Biochem Soc Symp 48:53–86

    Google Scholar 

  • Weber C, Farwick A, Benisch F, Bart D, Dietz H, Subtil T, Boles E (2010) Trends and challenges in the microbial production of lignocellulosic bioalcohol fuels. Appl Microbiol Biotechnol 87:1303–1315

    Article  CAS  Google Scholar 

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

    Article  Google Scholar 

  • Yang S, Pappas KM, Hauser LJ, Land ML, Chen GL, Hurst GB, Pan C, Kouvelis VN, Typas MA, Pelletier DA, Klingeman DM, Chang YJ, Samatova NF, Brown SD (2009b) Improved genome annotation for Zymomonas mobilis. Nat Biotechnol 27(10):893–894

    Article  CAS  Google Scholar 

  • Yang S, Land ML, Klingeman DM, Pelletier DA, Lu T-YS, Martin SL, Guo H-B, Smith JC, Brown SD (2010) Paradigm for industrial strain improvement indentifies sodium acetate tolerance loci in Zymomonas mobilis and Saccharomyces cerevisiae. Proc Nat Acad Sci 107(23):10395–10400

    Article  CAS  Google Scholar 

Download references

Acknowledgements

This research was carried out with support of the Australian National Collaborative Research Infrastructure Strategy (NCRIS) Biofuels Sub-Program. Microarray data analyses were performed at the Ramaciotti Centre (The University of New South Wales, Australia).

Author information

Authors and Affiliations

  1. School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Kensington, 2052, Australia

    Young Jae Jeon, Zhao Xun, Ping Su & Peter L. Rogers

Authors
  1. Young Jae Jeon
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Zhao Xun
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Ping Su
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Peter L. Rogers
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Peter L. Rogers.

Additional information

Young Jae Jeon and Zhao Xun contributed equally to this research.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Jeon, Y.J., Xun, Z., Su, P. et al. Genome-wide transcriptomic analysis of a flocculent strain of Zymomonas mobilis . Appl Microbiol Biotechnol 93, 2513–2518 (2012). https://doi.org/10.1007/s00253-012-3948-9

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00253-012-3948-9

Keywords

Search

Navigation