Genome‐scale modeling and in silico analysis of ethanologenic bacteria Zymomonas mobilis

Abstract

Bioethanol has been recognized as a potential alternative energy source. Among various ethanol-producing microbes, Zymomonas mobilis has acquired special attention due to its higher ethanol yield and tolerance. However, cellular metabolism in Z. mobilis remains unclear, hindering its practical application for bioethanol production. To elucidate such physiological characteristics, we reconstructed and validated a genome-scale metabolic network (iZM363) of Z. mobilis ATCC31821 (ZM4) based on its annotated genome and biochemical information. The phenotypic behaviors and metabolic states predicted by our genome-scale model were highly consistent with the experimental observations of Z. mobilis ZM4 strain growing on glucose as well as NMR-measured intracellular fluxes of an engineered strain utilizing glucose, fructose, and xylose. Subsequent comparative analysis with Escherichia coli and Saccharomyces cerevisiae as well as gene essentiality and flux coupling analyses have also confirmed the functional role of pdc and adh genes in the ethanologenic activity of Z. mobilis, thus leading to better understanding of this natural ethanol producer. In future, the current model could be employed to identify potential cell engineering targets, thereby enhancing the productivity of ethanol in Z. mobilis.

Progress and perspective on lignocellulosic hydrolysate inhibitor tolerance improvement in Zymomonas mobilis

“…Considering that even simple modification in genome may switch cellular metabolism or redox balance and thereby decrease the overall yield of the system, sophisticated computational models should be developed to guide future genetic or metabolic engineering efforts in Z. mobilis (Kalnenieks et al 2014;Widiastuti et al 2011;Yadav et al 2012). In addition, with the rapid development of synthetic biology tools and strategies especially the recent breakthrough on yeast genome synthesis Xie et al 2017;Zhang et al 2017), it is advantageous and practical to develop ZM4 as a chassis microorganism through both genome minimization and genome synthesis approaches considering its excellent industrial features, small genome size of 2.06 Mb, and fascinating unique physiology.…”

“…As a model bioethanol producer, Zymomonas mobilis has attracted considerable attention over the past decades due to its excellent industrial characteristics, such as the unique Entner-Doudoroff (ED) pathway under anaerobic conditions resulting in low cell mass formation, high specific rate of sugar uptake, high ethanol yield, notable ethanol tolerance, and the generally regarded as safe (GRAS) status (Panesar et al 2006;Rogers et al 2007). Furthermore, the availability of multiple genome sequences for 12 Zymomonas strains with small genome size around 2 Mb (Seo et al 2005;Yang et al 2009a;Zhao et al 2012), multiple genome-scale metabolic models (Kalnenieks et al 2014;Pentjuss et al 2013;Widiastuti et al 2011), and versatile genetic engineering strategies (Jia et al 2013;Shui et al 2015;Tan et al 2016) also accelerates the research progress in Z. mobilis. Z. mobilis has also been engineered for the production of sorbitol, gluconic acid, levan, 2,3-butanediol, isobutanol, and other biochemicals, which is proposed as an ideal microbial chassis for future synthetic biology and biorefinery (He et al 2014;Yang et al 2016).…”

Comparative Analysis of Biochemical Network Reconstructions

“…Two genome-scale reconstructions of Zymomonas mobilis by Lee et al, (2010) having 615 metabolites and 600 reactions, and Widiastuti et al, (2011) having 773 metabolites and 747 reactions were compared.…”

Control of Lactobacillus plantarum Contamination in Bioethanol Fermentation by Adding Plantaricins

“…Bioethanol can be produced by many kinds of microorganisms, of which Saccharomyces cerevisiae is the most employed species for industrial production (Widiastuti et al, 2011). However, industrial-scale bioethanol fermentation is frequently stressed by bacterial contaminants (Muthaiyan et al, 2011).…”