Transcriptomic Profiles of Zymomonas mobilis 8b to Furfural Acute and Long-Term Stress in Both Glucose and Xylose Conditions

Shihui Yang; Mary Ann Franden; Xia Wang; Yat-Chen Chou; Yun Hu; Steven D Brown; Philip T Pienkos; Min Zhang

doi:10.3389/fmicb.2020.00013

Transcriptomic Profiles of Zymomonas mobilis 8b to Furfural Acute and Long-Term Stress in Both Glucose and Xylose Conditions

Front Microbiol. 2020 Jan 23:11:13. doi: 10.3389/fmicb.2020.00013. eCollection 2020.

Authors

Shihui Yang^{1

2}, Mary Ann Franden², Xia Wang¹, Yat-Chen Chou², Yun Hu¹, Steven D Brown^{3

4}, Philip T Pienkos², Min Zhang²

Affiliations

¹ State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, School of Life Sciences, Hubei University, Wuhan, China.
² National Bioenergy and Biosciences Centers, National Renewable Energy Laboratory, Golden, CO, United States.
³ Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.
⁴ BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States.

Abstract

Zymomonas mobilis 8b is an ethanologenic bacterium engineered to utilize both glucose and xylose. The impacts of lignocellulosic hydrolyzate inhibitors on the growth of Zymomonas mobilis 8b have been investigated. However, the molecular responses of these inhibitors have not been completely elucidated yet. In this study, molecular responses to furfural were investigated using transcriptomic approaches of both chip-based microarray and a directional mRNA-Seq. Furfural acute shock time-course experiment with 3 g/L furfural supplemented when cells reached exponential phase and stress response experiment in the presence of 2 g/L furfural from the beginning of fermentation were carried out to study the physiological and transcriptional profiles of short-term and long-term effects of furfural on 8b. Furfural negatively affected 8b growth in terms of final biomass and the fermentation time. Transcriptomic studies indicated that the response of 8b to furfural was dynamic and complex, and differences existed between short-term shock and long-term stress responses. However, the gene function categories were similar with most down-regulated genes related to translation and biosynthesis, while the furfural up-regulated genes were mostly related to general stress responses. Several gene candidates have been identified and genetic studies indicated that expression of ZMO0465 and cysteine synthase operon ZMO0003-0006 driven by its native promoter in a shuttle vector enhanced the furfural tolerance of 8b. In addition, the relationship between microarray and mRNA-Seq was compared with good correlations. The directional mRNA-Seq data not only provided the gene expression profiling, but also can be applied for transcriptional architecture improvement to identify and confirm operons, novel transcripts, hypothetical gene functions, transcriptional start sites, and promoters with different strength.

Keywords: Zymomonas mobilis 8b; directional mRNA-Seq; furfural; microarray; transcriptomics; xylose.