Abstract
Background Zymomonas mobilis ZM4 is a capable ethanologenic bacterium with high ethanol productivity and ethanol tolerance. Previous studies indicated that several stress-related proteins and changes in the ZM4 membrane lipid composition may contribute to ethanol tolerance. However, the molecular mechanisms of its ethanol stress response have not been elucidated fully.Methodology/Principal FindingsIn this study, ethanol stress responses were investigated using systems biology approaches. Medium supplementation with an initial 47 g/L (6% v/v) ethanol reduced Z. mobilis ZM4 glucose consumption, growth rate and ethanol productivity compared to that of untreated controls. A proteomic analysis of early exponential growth identified about one thousand proteins, or approximately 55% of the predicted ZM4 proteome. Proteins related to metabolism and stress response such as chaperones and key regulators were more abundant in the early ethanol stress condition. Transcriptomic studies indicated that the response of ZM4 to ethanol is dynamic, complex and involves many genes from all the different functional categories. Most down-regulated genes were related to translation and ribosome biogenesis, while the ethanol-upregulated genes were mostly related to cellular processes and metabolism. Transcriptomic data were used to update Z. mobilis ZM4 operon models. Furthermore, correlations among the transcriptomic, proteomic and metabolic data were examined. Among significantly expressed genes or proteins, we observe higher correlation coefficients when fold-change values are higher.ConclusionsOur study has provided insights into the responses of Z. mobilis to ethanol stress through an integrated “omics” approach for the first time. This systems biology study elucidated key Z. mobilis ZM4 metabolites, genes and proteins that form the foundation of its distinctive physiology and its multifaceted response to ethanol stress.
Highlights
A number of countries around the world have set targets to displace substantial amounts of gasoline with lignocellulosic ethanol
This systems biology study elucidated key Z. mobilis ZM4 metabolites, genes and proteins that form the foundation of its distinctive physiology and its multifaceted response to ethanol stress
Z. mobilis are Gram-negative facultative anaerobic ethanologenic bacteria with a number of desirable industrial characteristics, such as unique anaerobic use of the Entner-Doudoroff (ED) pathway that results in low cell mass formation, high-specific productivity and ethanol yield and high ethanol tolerances of up to 85 g/L (11% v/v) for continuous culture and up to 127 g/L (16% v/v) in batch culture [6,7,8,9,10,11]
Summary
A number of countries around the world have set targets to displace substantial amounts of gasoline with lignocellulosic ethanol (see reviews [1,2,3,4,5]). Z. mobilis recombinant cellulase expression and secretion has been reported [20], and there have been improvements in transformation efficiency by modifying DNA restriction-modification systems [21]. DNA microarray studies have provided insights into Z. mobilis growth under aerobic and anaerobic conditions [23], under sodium chloride and sodium acetate stress conditions [22], as well as under ethanol and furfural stress [24,25] that led to insights into its physiology, inhibitor tolerance, and electron transport [26]. Other studies have improved Z. mobilis tolerance to different inhibitors using overexpression of the native hfq gene [27] or Deinococcus radiodurans irrE gene [28]. The molecular mechanisms of its ethanol stress response have not been elucidated fully
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