Transcriptome analysis of Zymomonas mobilis ZM4 reveals mechanisms of tolerance and detoxification of phenolic aldehyde inhibitors from lignocellulose pretreatment

Authors: YI, XIA - East China University Of Science And Technology; GU, HANQI - US Department Of Agriculture (USDA); GOA, QIUQIANG - East China University Of Science And Technology; Liu, Zonglin; BAO, JIE - East China University Of Science And Technology

Submitted to: BMC Biotechnology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/3/2015
Publication Date: 9/22/2015
Publication URL: http://handle.nal.usda.gov/10113/62887
Citation: Yi, X., Gu, H., Gao, Q., Liu, Z.L., Bao, J. 2015. Transcriptome analysis of Zymomonas mobilis ZM4 reveals mechanisms of tolerance and detoxification of phenolic aldehyde inhibitors from lignocellulose pretreatment. Biotechnology for Biofuels. 8(1):153. doi: 10.1186/s13068-015-0333-9.

Interpretive Summary: Pretreatment of lignocellulosic materials generates numerous toxic compounds that inhibit microbial growth and subsequent fermentation. While major furan aldehydes such as furfural and 5-hydroxymethyl-2-furaldehyde (HMF) and week organic acids were comprehensively studied, microbial reactions to phenolic compounds are not well known. In this study, ARS scientist in collaboration with scientists from East China University of Science and Technology, investigated genome expression of ethanologenic bacterial strain in response to varied phenolic aldehydes and revealed mechanisms of the bacterial tolerance. This research identified key genes for the bacterium to reduce the toxic phenolic compounds and illustrated metabolic pathways for the detoxification. Over expression of these genes increased ethanol productivity and inhibitor tolerance. Results of this study suggested that the functional group of phenolic aldehyde, similar to the furan aldehydes for furfural and HMF, is the causing agent of cell toxicity rather than the aromatic group or the phenolic hydroxyl group of these phenolic compounds. New knowledge and tolerant genes identified from this study will aid understanding of mechanisms of the bacterial tolerance and development of the next-generation biocatalysts for advanced biofuels production.

Technical Abstract: Background: Phenolic aldehydes generated from lignocellulose pretreatment exhibited severe toxic inhibitions on microbial growth and fermentation. Numerous tolerance studies against furfural, 5-hydroxymethyl-2-furaldehyde (HMF), acetate, and ethanol were reported, but studies on inhibition of phenolic aldehyde inhibitors are rare. For ethanologenic strains, Zymomonas mobilis ZM4 is high in ethanol productivity and genetic manipulation feasibility, but sensitive to phenolic aldehyde inhibitors. Molecular mechanisms of tolerance for Z. mobilis toward phenolic aldehydes are not known. Results: We took the first insight into genomic response of Z. mobilis ZM4 to the phenolic aldehyde inhibitors derived from lignocellulose pretreatment. The results suggest that the toxicity to cells is caused by the functional group of phenolic aldehyde, similar to furfural and HMF, rather than aromatic groups or phenolic hydroxyl groups. Transcriptome response against 4-hydroxybenzaldehyde, syringaldehyde, and vanillin, representing phenolic groups H, S, and G, respectively, was investigated. The atlas of the important genes responsible for significantly enhanced and repressed genes at the genomic level was illustrated. 272 genes with twofold greater expressions than non-treated controls and 36 gene clusters in response to challenges of these phenolic aldehydes were identified. Several reductases encoded by MO1116, ZMO1696, and ZMO1885 were found to play the key roles in reducing phenolic aldehydes into the corresponding phenolic alcohols. Reduction of phenolic aldehydes by overexpression of ZMO1116, ZMO1696, and ZMO1885 in Z. mobilis ZM4 resulted in the increased inhibitor conversion and ethanol productivity, especially for 4-hydroxybenzaldehyde and vanillin. Several transporter genes such as ZMO0282, ZMO0283, ZMO0798, ZMO0799, and ZMO0800 was also displayed significantly increased expressions against the phenolic aldehydes. Conclusions: The genes encoding reductases are with potentials on phenolic aldehydes-tolerant genes contributing to the reduction of phenolic aldehydes into the corresponding phenolic alcohols forms for Z. mobilis ZM4. Overexpression of the key genes improved the conversion ratio and ethanol productivity of 4-hydroxybenzaldehyde and vanillin with high toxicity. New knowledge obtained from this research aids understanding the mechanisms of bacterial tolerance and the development of the next-generation biocatalysts for advanced biofuels production.