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Escherichia coli W shows fast, highly oxidative sucrose metabolism and low acetate formation

  • Applied microbial and cell physiology
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Abstract

Sugarcane is the most efficient large-scale crop capable of supplying sufficient carbon substrate, in the form of sucrose, needed during fermentative feedstock production. However, sucrose metabolism in Escherichia coli is not well understood because the two most common strains, E. coli K-12 and B, do not grow on sucrose. Here, using a sucrose utilizing strain, E. coli W, we undertake an in-depth comparison of sucrose and glucose metabolism including growth kinetics, metabolite profiling, microarray-based transcriptome analysis, labelling-based proteomic analysis and 13C-fluxomics. While E. coli W grew comparably well on sucrose and glucose integration of the omics, datasets showed that during growth on each carbon source, metabolism was distinct. The metabolism was generally derepressed on sucrose, and significant flux rearrangements were observed in central carbon metabolism. These included a reduction in the flux of the oxidative pentose phosphate pathway branch, an increase in the tricarboxylic acid cycle flux and a reduction in the glyoxylate shunt flux due to the dephosphorylation of isocitrate dehydrogenase. But unlike growth on other sugars that induce cAMP-dependent Crp regulation, the phosphoenol-pyruvate-glyoxylate cycle was not active on sucrose. Lower acetate accumulation was also observed in sucrose compared to glucose cultures. This was linked to induction of the acetate catabolic genes actP and acs and independent of the glyoxylic shunt. Overall, the cells stayed highly oxidative. In summary, sucrose metabolism was fast, efficient and led to low acetate accumulation making it an ideal carbon source for industrial fermentation with E. coli W.

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Acknowledgments

We acknowledge the Australian Government’s overseas aid program (AusAID) and the Cooperative Research Centre for Sugar Industry Innovation through Biotechnology (CRC SIIB) for the funding. We thank Dr Katia Nones in the Microarray Facility of Institute of Molecular Biosciences, University of Queensland for her contribution in the microarray analysis, Dr Shana Jacob and Mr Michael Wang from Metabolomics Australia – Brisbane node for their assistance in metabolite analysis via HPLC and GC/MS. We thank Amanda Nouwens and Alun Jones from the proteomics facility at SCMB and IMB for their support with proteomics. JOK received financial support from the Australian Research Council (DE120101549)

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  1. Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St. Lucia, QLD, 4072, Australia

    Yalun Arifin, Colin Archer, SooA Lim, Lake-Ee Quek, Haryadi Sugiarto, Esteban Marcellin, Claudia E. Vickers, Jens O. Krömer & Lars K. Nielsen

  2. Centre for Microbial Electrosynthesis (CEMES) Research Road (Bldg 60), The University of Queensland, St. Lucia, QLD, 4072, Australia

    Jens O. Krömer

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  1. Yalun Arifin
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  2. Colin Archer
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  3. SooA Lim
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  4. Lake-Ee Quek
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Correspondence to Jens O. Krömer.

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Yalun Arifin, Colin Archer and SooA Lim contributed equally to this work and are co-first authors.

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Arifin, Y., Archer, C., Lim, S. et al. Escherichia coli W shows fast, highly oxidative sucrose metabolism and low acetate formation. Appl Microbiol Biotechnol 98, 9033–9044 (2014). https://doi.org/10.1007/s00253-014-5956-4

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