Molecular mechanism of enhanced ethanol tolerance associated with hfq overexpression in Zymomonas mobilis

Zymomonas mobilis is a promising microorganism for industrial bioethanol production. However, ethanol produced during fermentation is toxic to Z. mobilis and affects its growth and bioethanol production. Although several reports demonstrated that the RNA-binding protein Hfq in Z. mobilis contributes to the tolerance against multiple lignocellulosic hydrolysate inhibitors, the role of Hfq on ethanol tolerance has not been investigated. In this study, hfq in Z. mobilis was either deleted or overexpressed and their effects on cell growth and ethanol tolerance were examined. Our results demonstrated that hfq overexpression improved ethanol tolerance of Z. mobilis, which is probably due to energy saving by downregulating flagellar biosynthesis and heat stress response proteins, as well as reducing the reactive oxygen species induced by ethanol stress via upregulating the sulfate assimilation and cysteine biosynthesis. To explore proteins potentially interacted with Hfq, the TEV protease mediated Yeast Endoplasmic Reticulum Sequestration Screening system (YESS) was established in Z. mobilis. YESS results suggested that Hfq may modulate the cytoplasmic heat shock response by interacting with the heat shock proteins DnaK and DnaJ to deal with the ethanol inhibition. This study thus not only revealed the underlying mechanism of enhanced ethanol tolerance by hfq overexpression, but also provided an alternative approach to investigate protein-protein interactions in Z. mobilis.

[1]  Qiaoning He,et al.  Cysteine supplementation enhanced inhibitor tolerance of Zymomonas mobilis for economic lignocellulosic bioethanol production. , 2022, Bioresource technology.

[2]  E. Sundberg,et al.  Bacterial Flagellar Filament: A Supramolecular Multifunctional Nanostructure , 2021, International journal of molecular sciences.

[3]  E. Elahi,et al.  Impact of hfq and sigE on the tolerance of Zymomonas mobilis ZM4 to furfural and acetic acid stresses , 2020, PloS one.

[4]  Lydia M. Contreras,et al.  Multiple Small RNAs Interact to Co-regulate Ethanol Tolerance in Zymomonas mobilis , 2020, Frontiers in Bioengineering and Biotechnology.

[5]  Min Zhang,et al.  Transcriptomic Profiles of Zymomonas mobilis 8b to Furfural Acute and Long-Term Stress in Both Glucose and Xylose Conditions , 2020, Frontiers in Microbiology.

[6]  F. Torres,et al.  Physiological effects of overexpressed sigma factors on fermentative stress response of Zymomonas mobilis , 2019, Brazilian Journal of Microbiology.

[7]  J. Coon,et al.  Multiomic Fermentation Using Chemically Defined Synthetic Hydrolyzates Revealed Multiple Effects of Lignocellulose-Derived Inhibitors on Cell Physiology and Xylose Utilization in Zymomonas mobilis , 2019, Front. Microbiol..

[8]  Yanli Zheng,et al.  Characterization and repurposing of the endogenous Type I-F CRISPR–Cas system of Zymomonas mobilis for genome engineering , 2019, Nucleic acids research.

[9]  Ruifu Yang,et al.  Hfq Globally Binds and Destabilizes sRNAs and mRNAs in Yersinia pestis , 2019, mSystems.

[10]  T. Yura.  Regulation of the heat shock response in Escherichia coli: history and perspectives. , 2019, Genes & genetic systems.

[11]  C. Arraiano,et al.  New molecular interactions broaden the functions of the RNA chaperone Hfq , 2019, Current Genetics.

[12]  R. Gutiérrez-Ríos,et al.  Phenotypic and genomic analysis of Zymomonas mobilis ZM4 mutants with enhanced ethanol tolerance , 2019, Biotechnology reports.

[13]  Xiaobing Jiang,et al.  New technologies provide more metabolic engineering strategies for bioethanol production in Zymomonas mobilis , 2019, Applied Microbiology and Biotechnology.

[14]  G. D’Errico,et al.  Zymomonas mobilis exopolysaccharide structure and role in high ethanol tolerance. , 2018, Carbohydrate polymers.

[15]  Qiaoning He,et al.  Progress and perspective on lignocellulosic hydrolysate inhibitor tolerance improvement in Zymomonas mobilis , 2018, Bioresources and Bioprocessing.

[16]  Yun Hu,et al.  Advances and prospects in metabolic engineering of Zymomonas mobilis. , 2018, Metabolic engineering.

[17]  K. Miura.  An Overview of Current Methods to Confirm Protein-Protein Interactions , 2018, Protein and peptide letters.

[18]  S. Gottesman,et al.  Small Regulatory RNAs in the Enterobacterial Response to Envelope Damage and Oxidative Stress , 2018, Microbiology spectrum.

[19]  S. Woodson,et al.  The Hfq chaperone helps the ribosome mature , 2018, The EMBO journal.

[20]  Sean J McIlwain,et al.  Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose-utilizing derivatives 8b and 2032 , 2018, Biotechnology for Biofuels.

[21]  Shihui Yang,et al.  Identification and Characterization of 5′ Untranslated Regions (5′UTRs) in Zymomonas mobilis as Regulatory Biological Parts , 2017, Front. Microbiol..

[22]  V. Scarlato,et al.  Regulation of heat-shock genes in bacteria: from signal sensing to gene expression output , 2017, FEMS microbiology reviews.

[23]  Min Zhang,et al.  Zymomonas mobilis as a model system for production of biofuels and biochemicals , 2016, Microbial biotechnology.

[24]  Aixia Zhang,et al.  Hfq: the flexible RNA matchmaker. , 2016, Current opinion in microbiology.

[25]  Qi-li Zhu,et al.  Using global transcription machinery engineering (gTME) to improve ethanol tolerance of Zymomonas mobilis , 2016, Microbial Cell Factories.

[26]  Jie Bao,et al.  Transcriptome analysis of Zymomonas mobilis ZM4 reveals mechanisms of tolerance and detoxification of phenolic aldehyde inhibitors from lignocellulose pretreatment , 2015, Biotechnology for Biofuels.

[27]  Y. Matsumura,et al.  Effect of Low-concentration Furfural on Sulfur Amino Acid Biosynthesis in Saccharomyces cerevisiae , 2015 .

[28]  Hyunjin Yoon,et al.  hfq Plays Important Roles in Virulence and Stress Adaptation in Cronobacter sakazakii ATCC 29544 , 2015, Infection and Immunity.

[29]  Han Qin,et al.  Zymomonas mobilis: a novel platform for future biorefineries , 2014, Biotechnology for Biofuels.

[30]  F. Narberhaus,et al.  A tricistronic heat shock operon is important for stress tolerance of Pseudomonas putida and conserved in many environmental bacteria. , 2014, Environmental microbiology.

[31]  Brian H. Davison,et al.  Elucidation of Zymomonas mobilis physiology and stress responses by quantitative proteomics and transcriptomics , 2014, Front. Microbiol..

[32]  W. Hess,et al.  Riboregulators and the role of Hfq in photosynthetic bacteria , 2014, RNA biology.

[33]  K. Yonekura,et al.  Post-Transcriptional Regulator Hfq Binds Catalase HPII: Crystal Structure of the Complex , 2013, PloS one.

[34]  Courtney M. Johnson,et al.  Systems Biology Analysis of Zymomonas mobilis ZM4 Ethanol Stress Responses , 2013, PloS one.

[35]  George Georgiou,et al.  Engineering of TEV protease variants by yeast ER sequestration screening (YESS) of combinatorial libraries , 2013, Proceedings of the National Academy of Sciences.

[36]  Qi-li Zhu,et al.  Transcriptome profiling of Zymomonas mobilis under ethanol stress , 2012, Biotechnology for Biofuels.

[37]  J. Vogel,et al.  Hfq and its constellation of RNA , 2011, Nature Reviews Microbiology.

[38]  J. Vogel,et al.  Contribution of Hfq to photooxidative stress resistance and global regulation in Rhodobacter sphaeroides , 2011, Molecular microbiology.

[39]  Ying Zhang,et al.  irrE, an exogenous gene from Deinococcus radiodurans, improves the growth of and ethanol production by a Zymomonas mobilis strain under ethanol and acid stress. , 2010, Journal of microbiology and biotechnology.

[40]  Dale A Pelletier,et al.  The Zymomonas mobilis regulator hfq contributes to tolerance against multiple lignocellulosic pretreatment inhibitors , 2010, BMC Microbiology.

[41]  Laura R. Jarboe,et al.  Furfural Inhibits Growth by Limiting Sulfur Assimilation in Ethanologenic Escherichia coli Strain LY180 , 2009, Applied and Environmental Microbiology.

[42]  D. G. Gibson,et al.  Enzymatic assembly of DNA molecules up to several hundred kilobases , 2009, Nature Methods.

[43]  S. Woodson,et al.  The rpoS mRNA leader recruits Hfq to facilitate annealing with DsrA sRNA. , 2008, RNA.

[44]  M. Yamada,et al.  Magnesium Ions Improve Growth and Ethanol Production of Zymomonas mobilis under Heat or Ethanol Stress , 2007 .

[45]  P. Rogers,et al.  Zymomonas mobilis for fuel ethanol and higher value products. , 2007, Advances in biochemical engineering/biotechnology.

[46]  Hyun Seok Park,et al.  The genome sequence of the ethanologenic bacterium Zymomonas mobilis ZM4 , 2005, Nature Biotechnology.

[47]  K. Ohnishi,et al.  Gene fliA encodes an alternative sigma factor specific for flagellar operons in Salmonella typhimurium , 1990, Molecular and General Genetics MGG.

[48]  P. Bertin,et al.  Regulation cascade of flagellar expression in Gram-negative bacteria. , 2003, FEMS microbiology reviews.

[49]  K. Nakahigashi,et al.  Regulation of the heat-shock response. , 1999, Current opinion in microbiology.

[50]  T. Okamoto,et al.  Simple and Highly Efficient Transformation Method for Zymomonas mobilis: Electroporation. , 1992, Bioscience, biotechnology, and biochemistry.