The main bottleneck in the return of industrial butanol production from renewable feedstock through acetone-butanol-ethanol (ABE) fermentation by clostridia, such as Clostridium beijerinckii, is the low final butanol concentration. The problem is caused by the high toxicity of butanol to the production cells, and therefore, understanding the mechanisms by which clostridia react to butanol shock is of key importance. Detailed analyses of transcriptome data that were obtained after butanol shock and their comparison with data from standard ABE fermentation have resulted in new findings, while confirmed expected population responses. Although butanol shock resulted in upregulation of heat shock protein genes, their regulation is different than was assumed based on standard ABE fermentation transcriptome data. While glucose uptake, glycolysis, and acidogenesis genes were downregulated after butanol shock, solventogenesis genes were upregulated. Cyclopropanation of fatty acids and formation of plasmalogens seem to be significant processes involved in cell membrane stabilization in the presence of butanol. Surprisingly, one of the three identified Agr quorum-sensing system genes was upregulated. Upregulation of several putative butanol efflux pumps was described after butanol addition and a large putative polyketide gene cluster was found, the transcription of which seemed to depend on the concentration of butanol.

Department of Biomedical Engineering Brno University of Technology Brno Czech Republic

Department of Biotechnology University of Chemistry and Technology Prague Prague Czech Republic

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Alsaker, K. V. , Paredes, C. , & Papoutsakis, E. T. (2010). Metabolite stress and tolerance in the production of biofuels and chemicals: Gene‐expression‐based systems analysis of butanol, butyrate, and acetate stresses in the anaerobe PubMed DOI

Baerends, R. J. S. , Smits, W. K. , de Jong, A. , Hamoen, L. W. , Kok, J. , & Kuipers, O. P. (2004). Genome2D: A visualization tool for the rapid analysis of bacterial transcriptome data. Genome Biology, 5(5), R37 10.1186/gb-2004-5-5-r37 PubMed DOI PMC

Baumann, N. A. , Hagen, P. O. , & Goldfine, H. (1965). Phospholipids of PubMed

Behnken, S. , & Hertweck, C. (2012). Cryptic polyketide synthase genes in non‐pathogenic PubMed DOI PMC

Branska, B. , Fortova, L. , Dvorakova, M. , Liu, H. , Patakova, P. , Zhang, J. , & Melzoch, M. (2020). Chicken feather and wheat straw hydrolysate for direct utilization in biobutanol production. Renewable Energy, 145, 1941–1948. 10.1016/j.renene.2019.07.094 DOI

Branska, B. , Pechacova, Z. , Kolek, J. , Vasylkivska, M. , & Patakova, P. (2018). Flow cytometry analysis of PubMed DOI PMC

Chang, Y. , & Cronan, J. E. (1999). Membrane cyclopropane fatty acid content is a major factor in acid resistance of PubMed DOI

Cruz‐Morales, P. , Orellana, C. A. , Moutafis, G. , Moonen, G. , Rincon, G. , Nielsen, L. K. , & Marcellin, E. (2019). Revisiting the evolution and taxonomy of PubMed DOI PMC

De Mendoza, D. , Schujman, G. E. , & Aguilar, P. S. (2002). Biosynthesis and function of membrane lipids In Sonenshein A., Losick R., & Hoch J. (Eds.), Bacillus subtilis and its closest relatives (pp. 43–55). American Society of Microbiology.

Deng, W. , Li, C. , & Xie, J. (2013). The underling mechanism of bacterial TetR/AcrR family transcriptional repressors. Cellular Signalling, 25(7), 1608–1613. 10.1016/j.cellsig.2013.04.003 PubMed DOI

Ezeji, T. , Qureshi, N. , & Blaschek, H. P. (2007). Butanol production from agricultural residues: Impact of degradation products on PubMed DOI

Fisher, M. A. , Boyarskiy, S. , Yamada, M. R. , Kong, N. , Bauer, S. , & Tullman‐Ercek, D. (2014). Enhancing tolerance to short‐chain alcohols by engineering the PubMed DOI

Goldfine, H. (2010). The appearance, disappearance and reappearance of plasmalogens in evolution. Progress in Lipid Research, 49(4), 493–498. 10.1016/j.plipres.2010.07.003 PubMed DOI

Goldfine, H. , & Johnston, N. (2005). Membrane lipids of

Goodson, J. R. , Klupt, S. , Zhang, C. , Straight, P. , & Winkler, W. C. (2017). LoaP is a broadly conserved antiterminator protein that regulates antibiotic gene clusters in PubMed DOI PMC

Han, X. , & Gross, R. W. (1990). Plasmenylcholine and phosphatidylcholine membrane bilayers possess distinct conformational motifs. Biochemistry, 29(20), 4992–4996. 10.1021/bi00472a032 PubMed DOI

Herman, N. A. , Kim, S. J. , Li, J. S. , Cai, W. , Koshino, H. , & Zhang, W. (2017). The industrial anaerobe PubMed DOI PMC

Ingram, L. O. , & Buttke, T. M. (1985). Effects of alcohols on microorganisms. Advances in Microbial Physiology, 25, 253–300. 10.1016/S0065-2911(08)60294-5 PubMed DOI

Janssen, H. , Grimmler, C. , Ehrenreich, A. , Bahl, H. , & Fischer, R. J. (2012). A transcriptional study of acidogenic chemostat cells of PubMed DOI

Johnston, N. C. , Goldfine, H. , Malthaner, M. , & Seelig, J. (1987). 2H‐NMR studies on ether lipid‐rich bacterial membranes: Deuterium order profile of PubMed DOI

Kim, H. J. , Hwang, N. R. , & Lee, K. J. (2007). Heat shock responses for understanding diseases of protein denaturation. Molecules and Cells, 23(2), 123–131. PubMed

Koga, Y. , & Goldfine, H. (1984). Biosynthesis of phospholipids in PubMed PMC

Kolek, J. , Patakova, P. , Melzoch, K. , Sigler, K. , & Rezanka, T. (2015). Changes in membrane plasmalogens of PubMed DOI PMC

Lee, J. , & Blaschek, H. P. (2001). Glucose uptake in PubMed PMC

Lee, J. , Mitchell, W. J. , Tangney, M. , & Blaschek, H. P. (2005). Evidence for the presence of an alternative glucose transport system in PubMed DOI PMC

Lee, S. Y. , Park, J. H. , Jang, S. H. , Nielsen, L. K. , Kim, J. , & Jung, K. S. (2008). Fermentative butanol production by clostridia. Biotechnology and Bioengineering, 101(2), 209–228. 10.1002/bit.22003 PubMed DOI

Lepage, C. , Fayolle, F. , Hermann, M. , & Vandecasteele, J. P. (1987). Changes in membrane lipid composition of DOI

Letzel, A. C. , Pidot, S. J. , & Hertweck, C. (2013). A genomic approach to the cryptic secondary metabolome of the anaerobic world. Natural Product Reports, 30(3), 392–428. 10.1039/c2np20103h PubMed DOI

Liao, Y. , Smyth, G. K. , & Shi, W. (2014). FeatureCounts: An efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics, 30(7), 923–930. 10.1093/bioinformatics/btt656 PubMed DOI

Liao, Z. , Zhang, Y. , Luo, S. , Suo, Y. , Zhang, S. , & Wang, J. (2017). Improving cellular robustness and butanol titers of PubMed DOI

Love, M. I. , Huber, W. , & Anders, S. (2014). Moderated estimation of fold change and dispersion for RNA‐seq data with DESeq2. Genome Biology, 15(12), 550 10.1186/s13059-014-0550-8 PubMed DOI PMC

MacDonald, D. L. , & Goldfine, H. (1991). Effects of solvents and alcohols on the polar lipid composition of PubMed PMC

Maiti, S. , Sarma, S. J. , Brar, S. K. , Le Bihan, Y. , Drogui, P. , Buelna, G. , & Verma, M. (2016). Agro‐industrial wastes as feedstock for sustainable bio‐production of butanol by DOI

Mann, M. S. , Dragovic, Z. , Schirrmacher, G. , & Lutke‐Eversloh, T. (2012). Over‐expression of stress protein‐encoding genes helps PubMed DOI

Martin, W. F. , & Sousa, F. L. (2016). Early microbial evolution: The age of anaerobes. Cold Spring Harbor Perspectives in Biology, 8(2), a018127 10.1101/cshperspect.a018127 PubMed DOI PMC

Moon, H. G. , Jang, Y. S. , Cho, C. , Lee, J. , Binkley, R. , & Lee, S. Y. (2016). One hundred years of clostridial butanol fermentation. FEMS Microbiology Letters, 363(3), fnw001 10.1093/femsle/fnw001 PubMed DOI

Mukhopadhyay, A. (2015). Tolerance engineering in bacteria for the production of advanced biofuels and chemicals. Trends in Microbiology, 23(8), 498–508. 10.1016/j.tim.2015.04.008 PubMed DOI

Murarka, P. , Bagga, T. , Singh, P. , Rangra, S. , & Srivastava, P. (2019). Isolation and identification of a TetR family protein that regulates the biodesulfurization operon. AMB Express, 9(1), 71 10.1186/s13568-019-0801-x PubMed DOI PMC

Nguyen Le Minh, P. , de Cima, S. , Bervoets, I. , Maes, D. , Rubio, V. , & Charlier, D. (2015). Ligand binding specificity of RutR, a member of the TetR family of transcription regulators in PubMed DOI PMC

Patakova, P. , Branska, B. , Sedlar, K. , Vasylkivska, M. , Jureckova, K. , Kolek, J. , Koscova, P. , & Provaznik, I. (2019). Acidogenesis, solventogenesis, metabolic stress response and life cycle changes in PubMed DOI PMC

Patakova, P. , Kolek, J. , Sedlar, K. , Koscova, P. , Branska, B. , Kupkova, K. , Paulova, L. , & Provaznik, I. (2018). Comparative analysis of high butanol tolerance and production in clostridia. Biotechnology Advances, 36(3), 721–738. 10.1016/j.biotechadv.2017.12.004 PubMed DOI

Pini, C. , Bernal, P. , Godoy, P. , Ramos, J. , & Segura, A. (2009). Cyclopropane fatty acids are involved in organic solvent tolerance but not in acid stress resistance in PubMed DOI PMC

Robinson, M. D. , McCarthy, D. J. , & Smyth, G. K. (2010). EdgeR: A Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics, 26(1), 139–140. 10.1093/bioinformatics/btp616 PubMed DOI PMC

Sardessai, Y. , & Bhosle, S. (2002). Tolerance of bacteria to organic solvents. Research in Microbiology, 153(5), 263–268. 10.1016/S0923-2508(02)01319-0 PubMed DOI

Sedlar, K. , Kolek, J. , Gruber, M. , Jureckova, K. , Branska, B. , Csaba, G. , Vasylkivska, M. , Zimmer, R. , Patakova, P. , & Provaznik, I. (2019). A transcriptional response of PubMed DOI PMC

Sedlar, K. , Kolek, J. , Provaznik, I. , & Patakova, P. (2017). Reclassification of non‐type strain PubMed DOI

Sedlar, K. , Kolek, J. , Skutkova, H. , Branska, B. , Provaznik, I. , & Patakova, P. (2015). Complete genome sequence of PubMed DOI

Sedlar, K. , Koscova, P. , Vasylkivska, M. , Branska, B. , Kolek, J. , Kupkova, K. , Patakova, P. , & Provaznik, I. (2018). Transcription profiling of butanol producer PubMed DOI PMC

Shi, Z. , & Blaschek, H. P. (2008). Transcriptional analysis of PubMed DOI PMC

Sikkema, J. , de Bont, J. A. , & Poolman, B. (1995). Mechanisms of membrane toxicity of hydrocarbons. Microbiological Reviews, 59(2), 201–222. PubMed PMC

Tomas, C. A. , Beamish, J. , & Papoutsakis, E. T. (2004). Transcriptional analysis of butanol stress and tolerance in PubMed DOI PMC

Tomas, C. A. , Welker, N. E. , & Papoutsakis, E. T. (2003). Overexpression of PubMed DOI PMC

Vasylkivska, M. , Jureckova, K. , Branska, B. , Sedlar, K. , Kolek, J. , Provaznik, I. , & Patakova, P. (2019). Transcriptional analysis of amino acid, metal ion, vitamin and carbohydrate uptake in butanol‐producing PubMed DOI PMC

Vollherbst Schneck, K. , Sands, J. A. , & Montenecourt, B. S. (1984). Effect of butanol on lipid composition and fluidity of PubMed PMC

Zhao, Y. , Hindorff, L. A. , Chuang, A. , Monroe‐Augustus, M. , Lyristis, M. , Harrison, M. L. , Rudolph, F. B. , & Bennett, G. N. (2003). Expression of a cloned cyclopropane fatty acid synthase gene reduces solvent formation in PubMed DOI PMC

Zuber, U. , Drzewiecki, K. , & Hecker, M. (2001). Putative sigma factor SigI (YkoZ) of PubMed DOI PMC

Identification and Validation of Reference Genes in Clostridium beijerinckii NRRL B-598 for RT-qPCR Using RNA-Seq Data