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

Abstract

Backgroud: Acetic acid and furfural are two major inhibitors during lignocellulosic ethanol production. In our previous study, we successfully constructed an engineered Zymomonas mobilis ZM532 strain tolerant these double inhibitors by genome shuffling, but the molecular mechanisms of tolerance to these inhibitors are still unknown. This study investigated the responses of ZM532 and wild-type ZM4 to acetic acid and furfural using genomics, transcriptomics and label free quantitative proteomics. Results: By Sanger sequencing technology we re-verified of previously identified 19 mutations in ZM532, but we found a total of 23 single nucleotide polymorphisms (SNPs) in the coding sequence (CDS; 4) and intergenic region (19) in ZM532. Six SNPs were novel in this study. We also identified a total of 1865 and 14 novel differentially expressed genes (DEGs) in ZM532 and wild-type ZM4. Among these, 352 DEGs were up-regulated; while and 393 were down-regulated in AF_ZM532 vs RM_532, respectively. However, 442 DEGs were up while 463 were down-regulated in AF_ZM4 vs RM_ZM4. Moreover, 2 up and 8 down-regulated genes were identified in AF_ZM532 vs AF_ZM4; while 7 up and 1 down-regulated genes were found in RM_ZM532 vs RM_ZM. We also identified 1,532 proteins among 107 up and 204 down-regulated proteins detected in ZM4_AF vs ZM4_RM, 123 up and 205 down regulated proteins were identified in ZM532_AF vs ZM532_RM, respectively. In addition, a total of 16 up and 5 down-regulated proteins were identified out of 1462 in ZM4_AF vs ZM532_AF, while 8 up and 5 down-regulated proteins were observed out of 1491 in ZM4_RM vs ZM532_RM. These proteins and genes are involved in amino acid biosynthesis, macromolecules repair, glycolysis, flagella assembly, ABC transporter, fermentation, and ATP synthesis pathways and stress response. These mentioned genes and proteins confirmed and help to unravel the acetic acid and furfural tolerance mechanism between ZM532 and wild-type ZM4. May be these proteins and genes play key roles in ZM532 regulation with strong expressions under acids stress conditions. Furthermore, we knocked-out and overexpressed two differentially expressed genes (DEGs), ZMO_RS02740 up-regulated and ZMO_RS06525 down-regulated to investigate their roles in acetic acid and furfural tolerance. Our knockout and complementary experiments revealed that up-regulated expression gene ZMO_RS02740 and the down-regulated expression gene ZMO_RS06525 play important roles in dealing with furfural and acetic acid stress. Conclusion: ZM532 can be used to substitute ZM4 as a biocatalyst for bioethanol under acetic acid and furfural condition, with a shorter fermentation time and higher productivity. Further studies may be required to clarify the relationship between the acid resistance and the genetic disparity of mutant strains.

Genomic insights into clostridia in bioenergy production: Comparison of metabolic capabilities and evolutionary relationships

“…The analysis of furfural degradation enzymes reveals that the enzyme 2,5‐furandicarboxylate decarboxylase 1 ( hmfF ) is only present in Dca , Csp1 , and Mth2 strains (Sheet 9 of ESM3). This enzyme plays a crucial role in furfural degradation (Qin et al, 2016; Shabbir et al, 2023). The limited distribution of this enzyme across strains suggests that these particular strains may have specialized capabilities for furfural detoxification, which could be a valuable feature for biotechnological applications (Lopes et al, 2018; Zhang et al, 2013).…”

Comprehensive network of stress-induced responses in Zymomonas mobilis during bioethanol production: from physiological and molecular responses to the effects of system metabolic engineering

“…5 Systems metabolic engineering. Schematic view of systems metabolic engineering and its combination with classical metabolic engineering methods, systems biology and computational modeling, synthetic biology, and Adaptive laboratory evolution molecular chaperones (peptidylprolyl isomerase and the Hsp20 family protein) were up-regulated, leading to tolerance in mutant strains, especially ZM532 [104]. Besides reports on overexpression of transcriptional regulators, there are also other reports on the overexpression of exogenous transcriptional factors in Z. mobilis.…”