Discovery of Ethanol-Responsive Small RNAs in Zymomonas mobilis

Abstract

bZymomonas mobilis is a bacterium that can produce ethanol by fermentation. Due to its unique metabolism and efficient ethanol production, Z. mobilis has attracted special interest for biofuel energy applications; an important area of study is the regulation of those specific metabolic pathways. Small RNAs (sRNAs) have been studied as molecules that function as transcriptional regulators in response to cellular stresses. While sRNAs have been discovered in various organisms by computational prediction and experimental approaches, their discovery in Z. mobilis has not yet been reported. In this study, we have applied transcriptome analysis and computational predictions to facilitate identification and validation of 15 novel sRNAs in Z. mobilis. We furthermore characterized their expression in the context of high and low levels of intracellular ethanol. Here, we report that 3 of the sRNAs (Zms2, Zms4, and Zms6) are differentially expressed under aerobic and anaerobic conditions, when low and high ethanol productions are observed, respectively. Importantly, when we tested the effect of ethanol stress on the expression of sRNAs in Z. mobilis, Zms2, Zms6, and Zms18 showed differential expression under 5% ethanol stress conditions. These data suggest that in this organism regulatory RNAs can be associated with metabolic functions involved in ethanol stress responses.

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

“…For example, small RNAs (sRNAs) and 5′UTR in Z. mobilis have been studied recently by transcriptomics and bioinformatics approaches, and the result suggested that sRNAs potentially can be developed as novel biological parts to improve the tolerance against various inhibitors in Z. mobilis (Cho et al 2014(Cho et al , 2017.…”

Optimization of a novel biophysical model using large scale in vivo antisense hybridization data displays improved prediction capabilities of structurally accessible RNA regions

“…We selected two sRNAs responsive in expression level to ethanol stress, Zms4 (280 nt) and Zms6 (304 nt) of Z. mobilis (44). A RIP-seq experiment was performed by tagging each sRNA with 2-MS2 RNA.…”

Regulatory mechanisms related to biofuel tolerance in producing microbes

“…Using transcriptome analysis combined with computational predictions, Cho et al . () identified and validated 15 novel sRNAs in Z. mobile under ethanol stress, and three of them (Zms2, Zms4 and Zms6) exhibited differential expression between aerobic and anaerobic conditions, when low and high ethanol yield was observed respectively. In addition, Zms2, Zms6 and Zms18 exhibited differential expression under 5% ethanol stress conditions, indicating that in Z. mobile , sRNAs may play an important role in ethanol tolerance (Cho et al .…”