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.
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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
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
Cleveland WS, Devlin SJ (1988) Locally-weighted regression: an approach to regression analysis by local fitting. J Am Stat Assoc 83(403):596–610
Cui X, Churchill GA (2003) Genome Biol 4(4):210–215
D'Argenio DA, Miller SI (2004) Cyclic di-GMP as a bacterial second messenger. Microbiology 150(8):2497–2502
Goodman AE, Rogers PL, Skotnicki ML (1982) Minimal medium for isolation of auxotrophic Zymomonas mutants. Appl Environ Microbiol 44(2):496–498
Hughes J, Ramsden DK, Boulby JM (1994) The role of cellulosics in chitosan flocculation of Zymomonas mobilis. Biotechnol Lett 8:541–546
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
Jenal U, Malone J (2006) Mechanisms of cyclic-di-GMP signalling in bacteria. Ann Rev Genet 40:385–407
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
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
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
Lee JH, Skotnicki ML, Rogers PL (1982) Kinetic studies on a flocculent strain of Zymomonas mobilis. Biotechnol Lett 4:615–620
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
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
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
Skotnicki ML, Warr RG, Goodman AE, Lee KJ, Rogers PL (1984) High-productivity alcohol fermentation using Zymomonas mobilis. Biochem Soc Symp 48:53–86
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
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
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
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
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).
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Young Jae Jeon and Zhao Xun contributed equally to this research.
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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
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DOI: https://doi.org/10.1007/s00253-012-3948-9