Proteomic and metabolomic analysis of the cellular biomarkers related to inhibitors tolerance in Zymomonas mobilis ZM4

Abstract

BackgroundToxic compounds present in both the hydrolysate and pyrolysate of lignocellulosic biomass severely hinder the further conversion of lignocellulose-derived fermentable sugars into useful chemicals by common biocatalysts like Zymomonas mobilis, which has remarkable advantages over yeast. Although the extra detoxification treatment prior to fermentation process can help biocatalysts to eliminate the inhibitory environment, it is not environment friendly and cost effective for industrial application. As also reported by previous studies, an ideal and holistic approach to solve this issue is to develop microbial strains with inhibitor tolerance. However, previously engineered strains had the limitation that they could not cope well with the synergistic effect of multiple inhibitors as they are resistant only to a single inhibitor. Hence, understanding the universal cellular responses of Z. mobilis to various inhibitors may guide the designing of rational strategies to obtain more robust engineered strains for biofuel production from lignocellulosic biomass.ResultsQuantitative proteomics and metabolomics approaches were used to determine the cellular responses of Z. mobilis ZM4 to representative biomass-derived inhibitors like formic acid, acetic acid, furfural, 5-hydroxymethylfurfural, and phenol. The differentially expressed proteins identified under the challenge of single and combined inhibitors were involved in cell wall/membrane biogenesis, energy production, DNA replication, DNA recombination, DNA repair, DNA transcription, RNA translation, posttranslational modification, biosynthesis of amino acids, central carbon metabolism, etc. Metabolomics analysis showed that the up- or down-regulation pattern of metabolites was changed consistently with that of relevant proteins.ConclusionFifteen up-regulated proteins (e.g., Isopropylmalate isomerase LeuC, transcription-repair-coupling factor Mfd, and phosphoglucose isomerase PGI) and thirteen down-regulated proteins (e.g., TonB-dependent transporter ZMO1522, transcription termination factor Rho, and S1/P1 nuclease ZMO0127) were identified as candidate proteins related to all the stress conditions, implying that these proteins are potential biomarkers for the improvement of Z. mobilis ZM4 to resist complex biomass-derived inhibitors. These data can be used to generate a database of inhibitor-tolerance biomarkers, which could provide a basis for engineering Z. mobilis that would be able to grow in the presence of multiple inhibitors and directly ferment the biomass-derived sugars into biofuels.Electronic supplementary materialThe online version of this article (10.1186/s13068-018-1287-5) contains supplementary material, which is available to authorized users.

Molecular Mechanism of Engineered Zymomonas Mobilis Response to Furfural and Acetic acid Stress

“…The transcriptomics results demonstrated that genes encoding ABC transporters such as ZMO_RS08315, ZMO_RS04690, ZMO_RS01550, ZMO_RS02545 and ZMO_RS01130 were signi cantly up-regulated in ZM532 (Additional le 7, 8: Table S7, S8). The up-regulation of ABC transporter genes were consistent with results from acidic-pH treatment [41,42]. The up-regulation of ABC transporters may enhance and sustain the cytoplasmic pH homeostasis in mutant strain ZM532 under AF conditions.…”

“…The transcriptome pro le indicates ZMO_RS04970, ZMO_RS03175, ZMO_RS04970 were up-regulated in both strains and are involved in respiratory chain for energy production while ZMO_RS06760, ZMO_RS07025 and ZMO_RS02530 were down-regulated (Additional le 7, 8: Table S7, S8). Previous studies have con rmed that these proteins are essential of higher ethanol production and growth [42] however, up-and down-regulation of genes involved in various biological processes in response to various stressors.…”

“…Limiting agellum biosynthesis is an energy usage technique to reserve the comparatively expensive energy reserve in stress conditions. Moreover, proteins associated with chemotaxis and agellum were downregulated in E. coli under low-pH conditions and high-osmolality decreasing the agellum biosynthesis resulting in limited proton penetration [42].…”

Metabolic Engineering of Bacterial Respiration: High vs. Low P/O and the Case of Zymomonas mobilis

“…Interestingly, Ndh activity was shown to confer advantage for Z. mobilis aerobic growth and flocculation on minimal media (Jones-Burrage et al, 2019). Upregulation of ndh and some other oxidoreductase genes were observed under lignocellulose inhibitor stress (Chang et al, 2018). Hayashi et al (2015) demonstrated positive impact of Ndh activity on Z. mobilis salt stress resistance.…”

Phenotypic and genomic analysis of Zymomonas mobilis ZM4 mutants with enhanced ethanol tolerance

“…Z. mobilis has many desirable industrial characteristics, such as high-specific ethanol productivity, high ethanol yield, high ethanol tolerance and a wide fermentation pH range [ 2 , 3 , [6] , [7] , [8] ]. Metabolic engineering can provide new characteristics and capabilities to Z. mobilis like expand its substrate range, remove competing pathways and enhance its tolerance to ethanol and to other lignocellulosic hydrolysate inhibitors as aliphatic acids, furan aldehydes and furfural [ [9] , [10] , [11] ]. However, considering the variety of factors involved in the response to high concentrations of these compounds makes it difficult to devise new metabolic engineering strategies to generate tolerant strains, and for this reason still important to find novel genes and traits related to ethanol tolerance and to other biomass-derived growth inhibitors [ [8] , [9] , [10] , [11] , [12] ]…”