Skip to main content

Advertisement

SpringerLink
Log in

Elucidating butanol tolerance mediated by a response regulator Sll0039 in Synechocystis sp. PCC 6803 using a metabolomic approach

  • Genomics, transcriptomics, proteomics
  • Published:
Applied Microbiology and Biotechnology Aims and scope Submit manuscript

Abstract

Butanol is highly toxic to cyanobacterial cells, which could restrict the future application of this renewable system in producing carbon neutral biofuel butanol. To seek knowledge regarding butanol tolerance in cyanobacteria, a library of response regulator (RR) gene mutants of Synechocystis sp. PCC 6803 was screened. The results showed that the deletion mutant of an orphan RR-encoding genes ll0039 was more sensitive to butanol than the wild type, while complementation of the ∆slr1037 mutant with the sll0039 gene recovered its tolerance to the same level as the wild type, suggesting that the sll0039 gene was involved in the regulation of tolerance against butanol. Further analysis employing an integrated liquid chromatography-mass spectrometry (LC-MS)-based and gas chromatography-mass spectrometry (GC-MS)-based metabolomics was conducted to determine the possible regulatory network of butanol tolerance mediated by Sll0039. LC-MS analysis allowed the identification of several metabolites, such as adenosine 5′-diphosphate (ADP)-glucose, dihydroxyacetone phosphate (DHAP), d-ribose 5-phosphate (R5P), d-glucose 6-phosphate (G6P), d-fructose 6-phosphate (F6P), α-ketoglutaric acid (AKG), uridine 5′-diphospho (UDP)-glucose, and nicotinamide adenine dinucleotide phosphate (NADP), which were differentially regulated between the wild type and the ∆sll0039 mutant grown under butanol stress, while GC-MS analysis identified 1, 2, and 2 metabolic modules associated with the sll0039 gene deletion at 24, 48, and 72 h, respectively, suggesting that they were under control directly or indirectly by Sll0039 RR. In addition, a metabolomic comparison of the metabolic responses to butanol stress was conducted in the ∆sll0039 mutant and the ∆slr1037 mutant previously found to be involved in butanol tolerance (Chen et al. Biotechnol Biofuels 7:89 2014a), and the results showed that the regulatory networks mediated by Sll0039 and Slr1037 could be functionally independent in Synechocystis. The results provided a metabolomic description of the butanol tolerance network regulated by Sll0039.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6

Similar content being viewed by others

References

  • Alper H, Stephanopoulos G (2007) Global transcription machinery engineering: a new approach for improving cellular phenotype. Metab Eng 9(3):258–267

    Article  CAS  PubMed  Google Scholar 

  • Alper H, Moxley J, Nevoigt E, Fink GR, Stephanopoulos G (2006) Engineering yeast transcription machinery for improved ethanol tolerance and production. Science 314(5805):1565–1568

    Article  CAS  PubMed  Google Scholar 

  • Alsaker KV, Spitzer TR, Papoutsakis ET (2004) Transcriptional analysis of spo0A overexpression in Clostridium acetobutylicum and its effect on the cell’s response to butanol stress. J Bacteriol 186(7):1959–1971

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Anfelt J, Hallstrom B, Nielsen J, Uhlen M, Hudson EP (2013) Using transcriptomics to improve butanol tolerance. Appl Environ Microbiol 79:7419–7427

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Ashby MK, Houmard J (2006) Cyanobacterial two-component proteins: structure, diversity, distribution, and evolution. Microbiol Mol Biol Rev MMBR 70(2):472–509

    Article  CAS  Google Scholar 

  • Ball SG, Morell MK (2003) From bacterial glycogen to starch: understanding the biogenesis of the plant starch granule. Annu Rev Plant Biol 54:207–233

    Article  CAS  PubMed  Google Scholar 

  • Bennette NB, Eng JF, Dismukes GC (2011) An LC-MS-based chemical and analytical method for targeted metabolite quantification in the model cyanobacterium Synechococcus sp. PCC 7002. Anal Chem 83(10):3808–3816

    Article  CAS  PubMed  Google Scholar 

  • Brynildsen MP, Liao JC (2009) An integrated network approach identifies the isobutanol response network of Escherichia coli. Mol Syst Biol 5:277

    Article  PubMed Central  PubMed  Google Scholar 

  • Camsund D, Lindblad P (2014) Engineered transcriptional systems for cyanobacterial biotechnology. Front Bioeng Biotechnol 2:40

    Article  PubMed Central  PubMed  Google Scholar 

  • Chen L, Wu L, Wang J, Zhang W (2014a) Butanol tolerance regulated by a two-component response regulator Slr1037 in photosynthetic Synechocystis sp. PCC 6803. Biotechnol Biofuels 7:89

    Article  PubMed Central  PubMed  Google Scholar 

  • Chen L, Zhu Y, Song Z, Wang J, Zhang W (2014b) An orphan response regulator Sll0649 involved in cadmium tolerance and metal homeostasis in photosynthetic Synechocystis sp. PCC 6803. J Proteomics 103:87–102

    Article  CAS  PubMed  Google Scholar 

  • DiLeo MV, Strahan GD, den Bakker M, Hoekenga OA (2011) Weighted correlation network analysis (WGCNA) applied to the tomato fruit metabolome. PLoS One 6(10):e26683

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Dunlop MJ (2011) Engineering microbes for tolerance to next-generation biofuels. Biotechnol Biofuels 4:32

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Durre P (2007) Biobutanol: an attractive biofuel. Biotechnol J 2(12):1525–1534

    Article  PubMed  Google Scholar 

  • Durre P (2008) Fermentative butanol production: bulk chemical and biofuel. Ann N Y Acad Sci 1125:353–362

    Article  PubMed  Google Scholar 

  • Fiehn O (2002) Metabolomics—the link between genotypes and phenotypes. Plant Mol Biol 48:155–171

    Article  CAS  PubMed  Google Scholar 

  • Green EM (2011) Fermentative production of butanol—the industrial perspective. Curr Opin Biotechnol 22(3):337–343

    Article  CAS  PubMed  Google Scholar 

  • Grundel M, Scheunemann R, Lockau W, Zilliges Y (2012) Impaired glycogen synthesis causes metabolic overflow reactions and affects stress responses in the cyanobacterium Synechocystis sp. PCC 6803. Microbiology 158(Pt 12):3032–3043

    Article  PubMed  Google Scholar 

  • Hemamalini R, Khare S (2014) A proteomic approach to understand the role of the outer membrane porins in the organic solvent-tolerance of Pseudomonas aeruginosa PseA. PLoS One 9(8):e103788

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Hoch JA (2000) Two-component and phosphorelay signal transduction. Curr Opin Microbiol 3(2):165–170

    Article  CAS  PubMed  Google Scholar 

  • Huang HH, Camsund D, Lindblad P, Heidorn T (2010) Design and characterization of molecular tools for a synthetic biology approach towards developing cyanobacterial biotechnology. Nucleic Acids Res 38(8):2577–2593

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Jin H, Chen L, Wang J, Zhang W (2014) Engineering biofuel tolerance in non-native producing microorganisms. Biotechnol Adv 32(2):541–548

    Article  CAS  PubMed  Google Scholar 

  • Jozefczuk S, Klie S, Catchpole G, Szymanski J, Cuadros-Inostroza A, Steinhauser D, Selbig J, Willmitzer L (2010) Metabolomic and transcriptomic stress response of Escherichia coli. Mol Syst Biol 6:364

    Article  PubMed Central  PubMed  Google Scholar 

  • Kaczmarzyk D, Anfelt J, Sarnegrim A, Hudson EP (2014) Overexpression of sigma factor SigB improves temperature and butanol tolerance of Synechocystis sp. PCC6803. J Biotechnol 182–183:54–60

    Article  PubMed  Google Scholar 

  • Kim WY, Kang S, Kim BC, Oh J, Cho S, Bhak J, Choi JS (2008) SynechoNET: integrated protein-protein interaction database of a model cyanobacterium Synechocystis sp. PCC 6803. BMC Bioinformatics 9(Suppl 1):S20

    Article  PubMed Central  PubMed  Google Scholar 

  • Klahn S, Hagemann M (2011) Compatible solute biosynthesis in cyanobacteria. Environ Microbiol 13(3):551–562

    Article  PubMed  Google Scholar 

  • Lan EI, Liao JC (2011) Metabolic engineering of cyanobacteria for 1-butanol production from carbon dioxide. Metab Eng 13(4):353–363

    Article  CAS  PubMed  Google Scholar 

  • Lan EI, Liao JC (2012) ATP drives direct photosynthetic production of 1-butanol in cyanobacteria. Proc Natl Acad Sci U S A 109(16):6018–6023

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Langfelder P, Horvath S (2008) WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics 9:559

    Article  PubMed Central  PubMed  Google Scholar 

  • Ledauphin J, Le Milbeau C, Barillier D, Hennequin D (2010) Differences in the volatile compositions of French labeled brandies (Armagnac, Calvados, Cognac, and Mirabelle) using GC-MS and PLS-DA. J Agric Food Chem 58(13):7782–7793

    Article  CAS  PubMed  Google Scholar 

  • Lee SY, Park JH, Jang SH, Nielsen LK, Kim J, Jung KS (2008) Fermentative butanol production by Clostridia. Biotechnol Bioeng 101(2):209–228

    Article  CAS  PubMed  Google Scholar 

  • Liu J, Chen L, Wang J, Qiao J, Zhang W (2012) Proteomic analysis reveals resistance mechanism against biofuel hexane in Synechocystis sp. PCC 6803. Biotechnol Biofuels 5(1):68

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Liu ZX, Li HC, Wei YP, Chu WY, Chong YL, Long XH, Liu ZP, Qin S, Shao HB (2013) Signal transduction pathways in Synechocystis sp. PCC 6803 and biotechnological implications under abiotic stress. Crit Rev Biotechnol. doi:10.3109/07388551.2013.838662

  • Liu D, Chen Y, Ding FY, Zhao T, Wu JL, Guo T, Ren HF, Li BB, Niu HQ, Cao Z, Lin XQ, Xie JJ, He XJ, Ying HJ (2014) Biobutanol production in a Clostridium acetobutylicum biofilm reactor integrated with simultaneous product recovery by adsorption. Biotechnol Biofuels 7(1):5

    Article  PubMed Central  PubMed  Google Scholar 

  • Los DA, Zorina A, Sinetova M, Kryazhov S, Mironov K, Zinchenko VV (2010) Stress sensors and signal transducers in cyanobacteria. Sensors 10(3):2386–2415

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Ma R, Zhang Y, Hong H, Lu W, Lin M, Chen M, Zhang W (2011) Improved osmotic tolerance and ethanol production of ethanologenic Escherichia coli by IrrE, a global regulator of radiation-resistance of Deinococcus radiodurans. Curr Microbiol 62(2):659–664

    Article  CAS  PubMed  Google Scholar 

  • Maeda K, Narikawa R, Ikeuchi M (2014) CugP is a novel ubiquitous non-GalU-type bacterial UDP-glucose pyrophosphorylase found in cyanobacteria. J Bacteriol 196(13):2348–2354

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Miranda H, Cheregi O, Netotea S, Hvidsten TR, Moritz T, Funk C (2013) Co-expression analysis, proteomic and metabolomic study on the impact of a Deg/HtrA protease triple mutant in Synechocystis sp. PCC 6803 exposed to temperature and high light stress. J Proteomics 78:294–311

    Article  CAS  PubMed  Google Scholar 

  • Nicolaou SA, Gaida SM, Papoutsakis ET (2010) A comparative view of metabolite and substrate stress and tolerance in microbial bioprocessing: from biofuels and chemicals, to biocatalysis and bioremediation. Metab Eng 12(4):307–331

    Article  CAS  PubMed  Google Scholar 

  • Pal D, Khozin-Goldberg I, Didi-Cohen S, Solovchenko A, Batushansky A, Kaye Y, Sikron N, Samani T, Fait A, Boussiba S (2013) Growth, lipid production and metabolic adjustments in the euryhaline eustigmatophyte Nannochloropsis oceanica CCALA 804 in response to osmotic downshift. Appl Microbiol Biotechnol 97(18):8291–8306

  • Pollak N, Dolle C, Ziegler M (2007) The power to reduce: pyridine nucleotides—small molecules with a multitude of functions. Biochem J J402(2):205–218

    Google Scholar 

  • Qiao J, Wang J, Chen L, Tian X, Huang S, Ren X, Zhang W (2012) Quantitative iTRAQ LC-MS/MS proteomics reveals metabolic responses to biofuel ethanol in cyanobacterial Synechocystis sp. PCC 6803. J Proteome Res 11(11):5286–5300

    Article  CAS  PubMed  Google Scholar 

  • Ren Q, Shi M, Chen L, Wang J, Zhang W (2014) Integrated proteomic and metabolomic characterization of a novel two-component response regulator Slr 1909 involved in acid tolerance in Synechocystis sp. PCC 6803. J Proteomics 109C:76–89

    Article  Google Scholar 

  • Roessner U, Luedemann A, Brust D, Fiehn O, Linke T, Willmitzer L, Fernie A (2001) Metabolic profiling allows comprehensive phenotyping of genetically or environmentally modified plant systems. Plant Cell 13(1):11–29

  • Rutherford BJ, Dahl RH, Price RE, Szmidt HL, Benke PI, Mukhopadhyay A, Keasling JD (2010) Functional genomic study of exogenous n-butanol stress in Escherichia coli. Appl Environ Microbiol 76(6):1935–1945

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Schiel-Bengelsdorf B, Montoya J, Linder S, Durre P (2013) Butanol fermentation. Environ Technol 34(13–16):1691–1710

    Article  CAS  PubMed  Google Scholar 

  • Schwarz D, Orf I, Kopka J, Hagemann M (2013) Recent applications of metabolomics toward cyanobacteria. Metabolites 3(1):72–100

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Strøm AR, Kaasen I (1993) Trehalose metabolism in Escherichia coli stress protection and stress regulation of gene expression. Mol Microbiol 8(2):205–210

    Article  PubMed  Google Scholar 

  • Su Y, Wang J, Shi M, Niu X, Yu X, Gao L, Zhang X, Chen L, Zhang W (2014) Metabolomic and network analysis of astaxanthin-producing Haematococcus pluvialis under various stress conditions. Bioresour Technol 170:522–529

    Article  CAS  PubMed  Google Scholar 

  • Swan TM, Watson K (1999) Stress tolerance in a yeast lipid mutant: membrane lipids influence tolerance to heat and ethanol independently of heat shock proteins and trehalose. Can J Microbiol 45(6):472–479

    Article  CAS  PubMed  Google Scholar 

  • Tian X, Chen L, Wang J, Qiao J, Zhang W (2013) Quantitative proteomics reveals dynamic responses of Synechocystis sp. PCC 6803 to next-generation biofuel butanol. J Proteomics 78:326–345

    Article  CAS  PubMed  Google Scholar 

  • Tomas CA, Welker NE, Papoutsakis ET (2003) Overexpression of groESL in Clostridium acetobutylicum results in increased solvent production and tolerance, prolonged metabolism, and changes in the cell’s transcriptional program. Appl Environ Microbiol 69(8):4951–4965

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Van Dijck P, Colavizza D, Smet P, Thevelein JM (1995) Differential importance of trehalose in stress resistance in fermenting and nonfermenting Saccharomyces cerevisiae cells. Appl Environ Microbiol 61(1):109–115

    PubMed Central  PubMed  Google Scholar 

  • Wang HL, Postier BL, Burnap RL (2002) Optimization of fusion PCR for in vitro construction of gene knockout fragments. BioTechniques 33(1):26–32

    CAS  PubMed  Google Scholar 

  • Wang J, Chen L, Tian X, Gao L, Niu X, Shi M, Zhang W (2013) Global metabolomic and network analysis of Escherichia coli responses to exogenous biofuels. J Proteome Res 12(11):5302–5312

    Article  CAS  PubMed  Google Scholar 

  • Wang J, Zhang X, Shi M, Gao L, Niu X, Te R, Chen L, Zhang W (2014a) Metabolomic analysis of the salt-sensitive mutants reveals changes in amino acid and fatty acid composition important to long-term salt stress in Synechocystis sp. PCC 6803. Funct Integr Genom 14(2):431–440

    Article  CAS  Google Scholar 

  • Wang Y, Shi M, Niu X, Zhang X, Gao L, Chen L, Wang J, Zhang W (2014b) Metabolomic basis of laboratory evolution of butanol tolerance in photosynthetic Synechocystis sp. PCC 6803. Microb Cell Factories 13(1):151

    Article  Google Scholar 

  • Yoshihara S, Suzuki F, Fujita H, Geng XX, Ikeuchi M (2000) Novel putative photoreceptor and regulatory genes required for the positive phototactic movement of the unicellular motile cyanobacterium Synechocystis sp. PCC 6803. Plant Cell Physiol 41(12):1299–1304

    Article  CAS  PubMed  Google Scholar 

  • Zhang B, Horvath S (2005) A general framework for weighted gene co-expression network analysis. Stat Appl Genet Mol Biol 4:Article17

  • Zhu H, Ren X, Wang J, Song Z, Shi M, Qiao J, Tian X, Liu J, Chen L, Zhang W (2013) Integrated OMICS guided engineering of biofuel butanol-tolerance in photosynthetic Synechocystis sp. PCC 6803. Biotechnol Biofuels 6(1):106

    Article  CAS  PubMed Central  PubMed  Google Scholar 

Download references

Acknowledgments

The research was supported by grants from the National Basic Research Program of China (“973” program, project no. 2011CBA00803, no. 2014CB745101, and no. 2012CB721101), the National High-tech R&D Program (“863” program, project no. 2012AA02A707), and the National Science Foundation of China (NSFC, project no. 31470217).

Author information

Authors and Affiliations

  1. Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, People’s Republic of China

    Xiangfeng Niu, Ye Zhu, Guangsheng Pei, Lina Wu, Lei Chen & Weiwen Zhang

  2. Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, People’s Republic of China

    Xiangfeng Niu, Ye Zhu, Guangsheng Pei, Lina Wu, Lei Chen & Weiwen Zhang

  3. SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, 300072, People’s Republic of China

    Xiangfeng Niu, Ye Zhu, Guangsheng Pei, Lina Wu, Lei Chen & Weiwen Zhang

Authors
  1. Xiangfeng Niu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Ye Zhu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Guangsheng Pei
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Lina Wu
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Lei Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Weiwen Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Lei Chen or Weiwen Zhang.

Electronic supplementary material

Below is the link to the electronic supplementary material.

ESM 1

(PDF 1679 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Niu, X., Zhu, Y., Pei, G. et al. Elucidating butanol tolerance mediated by a response regulator Sll0039 in Synechocystis sp. PCC 6803 using a metabolomic approach. Appl Microbiol Biotechnol 99, 1845–1857 (2015). https://doi.org/10.1007/s00253-015-6374-y

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00253-015-6374-y

Keywords

Search

Navigation