Transcriptome profiling of Zymomonas mobilis under ethanol stress

Abstract

BackgroundHigh tolerance to ethanol is a desirable characteristics for ethanologenic strains used in industrial ethanol fermentation. A deeper understanding of the molecular mechanisms underlying ethanologenic strains tolerance of ethanol stress may guide the design of rational strategies to increase process performance in industrial alcoholic production. Many extensive studies have been performed in Saccharomyces cerevisiae and Escherichia coli. However, the physiological basis and genetic mechanisms involved in ethanol tolerance for Zymomonas mobilis are poorly understood on genomic level. To identify the genes required for tolerance to ethanol, microarray technology was used to investigate the transcriptome profiling of the ethanologenic Z. mobilis in response to ethanol stress.ResultsWe successfully identified 127 genes which were differentially expressed in response to ethanol. Ethanol up- or down-regulated genes related to cell wall/membrane biogenesis, metabolism, and transcription. These genes were classified as being involved in a wide range of cellular processes including carbohydrate metabolism, cell wall/membrane biogenesis, respiratory chain, terpenoid biosynthesis, DNA replication, DNA recombination, DNA repair, transport, transcriptional regulation, some universal stress response, etc.ConclusionIn this study, genome-wide transcriptional responses to ethanol were investigated for the first time in Z. mobilis using microarray analysis.Our results revealed that ethanol had effects on multiple aspects of cellular metabolism at the transcriptional level and that membrane might play important roles in response to ethanol. Although the molecular mechanism involved in tolerance and adaptation of ethanologenic strains to ethanol is still unclear, this research has provided insights into molecular response to ethanol in Z. mobilis. These data will also be helpful to construct more ethanol resistant strains for cellulosic ethanol production in the future.

Systems Biology Analysis of Zymomonas mobilis ZM4 Ethanol Stress Responses

“…1), which is consistent with a recent transcriptomic study for Z. mobilis under 5% ethanol stress published during the reviewing process of our manuscript [25]. In addition, both studies indicated that ethanol has effects on multiple aspects of cellular metabolism [25].…”

“…Gene deletions are possible in Z. mobilis [22]. 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].…”

Functional Characterization of CRISPR-Cas System in the Ethanologenic Bacterium <i>Zymomonas mobilis</i> ZM4

“…In E. coli, expression of the CRISPR array is revealed to be highly regulated [38]. In addition, the cas genes seem to express constitutionally which is inferred from the previous transcriptomic analysis in Z. mobilis ZM4 [33]- [35]. Taken together, the CRISPR-Cas system in ZM4 can be expressed under the normal growing condition.…”

“…Further, the transcripts of six cas genes in Z. mobilis ZM4 growing at various conditions could be easily detected in the previous transcriptional analysis [33] [34]. For example, the relative transcriptional levels of the cas genes are presented in Table 1, which is retrieved from the transcriptome data in the previous studies [35].…”

Discovery of Ethanol-Responsive Small RNAs in Zymomonas mobilis

“…To further characterize the uncovered sRNAs, we confirmed their expression levels under ethanol levels (5%) that have been reported to stress cell growth and decrease ethanol productivity (53). Three sRNAs (Zms2, Zms6, and Zms18) were expressed differentially under ethanol stress, suggesting that they could be related to regulatory mechanisms of ethanol production or tolerance in Z. mobilis.…”