Butanol tolerance regulated by a two-component response regulator Slr1037 in photosynthetic Synechocystis sp. PCC 6803

Biotechnology for Biofuels

Lei Chen¹  Lina Wu¹  Jiangxin Wang¹  Weiwen Zhang¹ 

[1] Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, P.R. China

关键词: Synechocystis;    Proteomics;    Response regulator;    Tolerance;    Butanol;   

Others  :  792210
DOI  :  10.1186/1754-6834-7-89

 received in 2013-12-23, accepted in 2014-05-27,  发布年份 2014

【 摘 要 】

Background

Butanol production directly from CO₂ in photosynthetic cyanobacteria is restricted by the high toxicity of butanol to the hosts. In previous studies, we have found that a few two-component signal transduction systems (TCSTSs) were differentially regulated in Synechocystis sp. PCC 6803 after butanol treatment.

Results

To explore regulatory mechanisms of butanol tolerance, in this work, by constructing gene knockout mutants of the butanol-responsive TCSTS genes and conducting tolerance analysis, we uncovered that an orphan slr1037 gene encoding a novel response regulator was involved in butanol tolerance in Synechocystis. Interestingly, the ∆slr1037 mutant grew similarly to the wild type under several other stress conditions tested, which suggests that its regulation on butanol tolerance is specific. Using a quantitative iTRAQ LC-MS/MS proteomics approach coupled with real-time reverse transcription PCR, we further determined the possible butanol-tolerance regulon regulated by Slr1037. The results showed that, after slr1037 deletion, proteins involved in photosynthesis and glycolysis/gluconeogenesis of central metabolic processes, and glutaredoxin, peptide methionine sulfoxide reductase and glucosylglycerol-phosphate synthase with stress-responsive functions were down-regulated, suggesting that Slr1037 may exhibit regulation to a wide range of cellular functions in combating butanol stress.

Conclusions

The study provided a proteomic description of the putative butanol-tolerance regulon regulated by the slr1037 gene. As the first signal transduction protein identified directly related to butanol tolerance, response regulator Slr1037 could be a natural candidate for transcriptional engineering to improve butanol tolerance in Synechocystis.

【 授权许可】

   
2014 Chen et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 2.

Figure 3.

Figure 4.

【 参考文献 】

• [1]Durre P: Biobutanol: an attractive biofuel. Biotechnol J 2007, 2:1525-1534.
• [2]Durre P, Fischer RJ, Kuhn A, Lorenz K, Schreiber W, Sturzenhofecker B, Ullmann S, Winzer K, Sauer U: Solventogenic enzymes of Clostridium acetobutylicum: catalytic properties, genetic organization, and transcriptional regulation. FEMS Microbiol Rev 1995, 17:251-262.
• [3]Lee SY, Park JH, Jang SH, Nielsen LK, Kim J, Jung KS: Fermentative butanol production by Clostridia. Biotechnol Bioeng 2008, 101:209-228.
• [4]Zheng YN, Li LZ, Xian M, Ma YJ, Yang JM, Xu X, He DZ: Problems with the microbial production of butanol. J Ind Microbiol Biotechnol 2009, 36:1127-1138.
• [5]Green EM: Fermentative production of butanol - the industrial perspective. Curr Opin Biotechnol 2011, 22:337-343.
• [6]Atsumi S, Cann AF, Connor MR, Shen CR, Smith KM, Brynildsen MP, Chou KJ, Hanai T, Liao JC: Metabolic engineering of Escherichia coli for 1-butanol production. Metab Eng 2008, 10:305-311.
• [7]Inui M, Suda M, Kimura S, Yasuda K, Suzuki H, Toda H, Yamamoto S, Okino S, Suzuki N, Yukawa H: Expression of Clostridium acetobutylicum butanol synthetic genes in Escherichia coli. Appl Microbiol Biotechnol 2008, 77:1305-1316.
• [8]Shen CR, Liao JC: Metabolic engineering of Escherichia coli for 1-butanol and 1-propanol production via the keto-acid pathways. Metab Eng 2008, 10:312-320.
• [9]Atsumi S, Hanai T, Liao JC: Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels. Nature 2008, 451:86-89.
• [10]Berezina OV, Zakharova NV, Brandt A, Yarotsky SV, Schwarz WH, Zverlov VV: Reconstructing the clostridial n-butanol metabolic pathway in Lactobacillus brevis. Appl Microbiol Biotechnol 2010, 87:635-646.
• [11]Machado IM, Atsumi S: Cyanobacterial biofuel production. J Biotechnol 2012, 162:50-56.
• [12]Lan EI, Liao JC: Metabolic engineering of cyanobacteria for 1-butanol production from carbon dioxide. Metab Eng 2011, 13:353-363.
• [13]Lan EI, Liao JC: ATP drives direct photosynthetic production of 1-butanol in cyanobacteria. Proc Natl Acad Sci U S A 2012, 109:6018-6023.
• [14]Nicolaou SA, Gaida SM, Papoutsakis ET: A comparative view of metabolite and substrate stress and tolerance in microbial bioprocessing: from biofuels and chemicals, to biocatalysis and bioremediation. Metab Eng 2010, 12:307-331.
• [15]Dunlop MJ: Engineering microbes for tolerance to next-generation biofuels. Biotechnol Biofuels 2011, 4:32. BioMed Central Full Text
• [16]Brynildsen MP, Liao JC: An integrated network approach identifies the isobutanol response network of Escherichia coli. Mol Syst Biol 2009, 5:277.
• [17]Rutherford BJ, Dahl RH, Price RE, Szmidt HL, Benke PI, Mukhopadhyay A, Keasling JD: Functional genomic study of exogenous n-butanol stress in Escherichia coli. Appl Environ Microbiol 2010, 76:1935-1945.
• [18]Alper H, Moxley J, Nevoigt E, Fink GR, Stephanopoulos G: Engineering yeast transcription machinery for improved ethanol tolerance and production. Science 2006, 314:1565-1568.
• [19]Alsaker KV, Spitzer TR, Papoutsakis ET: Transcriptional analysis of spo0A overexpression in Clostridium acetobutylicum and its effect on the cell's response to butanol stress. J Bacteriol 2004, 186:1959-1971.
• [20]Chen T, Wang J, Yang R, Li J, Lin M, Lin Z: Laboratory-evolved mutants of an exogenous global regulator, IrrE from Deinococcus radiodurans, enhance stress tolerances of Escherichia coli. PLoS One 2011, 6:e16228.
• [21]Zhang H, Chong H, Ching CB, Song H, Jiang R: Engineering global transcription factor cyclic AMP receptor protein of Escherichia coli for improved 1-butanol tolerance. Appl Microbiol Biotechnol 2012, 94:1107-1117.
• [22]Capra EJ, Laub MT: Evolution of two-component signal transduction systems. Annu Rev Microbiol 2012, 66:325-347.
• [23]Bekker M, de Teixeira MM, Hellingwerf KJ: The role of two-component regulation systems in the physiology of the bacterial cell. Sci Prog 2006, 89:213-242.
• [24]Liu J, Chen L, Wang J, Qiao J, Zhang W: Proteomic analysis reveals resistance mechanism against biofuel hexane in Synechocystis sp. PCC 6803. Biotechnol Biofuels 2012, 5:68. BioMed Central Full Text
• [25]Wang J, Chen L, Huang S, Liu J, Ren X, Tian X, Qiao J, Zhang W: RNA-seq based identification and mutant validation of gene targets related to ethanol resistance in cyanobacterial Synechocystis sp. PCC 6803. Biotechnol Biofuels 2012, 5:89. BioMed Central Full Text
• [26]Tian X, Chen L, Wang J, Qiao J, Zhang W: Quantitative proteomics reveals dynamic responses of Synechocystis sp. PCC 6803 to next-generation biofuel butanol. J Proteomics 2013, 78:326-345.
• [27]Qiao J, Wang J, Chen L, Tian X, Huang S, Ren X, Zhang W: Quantitative iTRAQ LC-MS/MS proteomics reveals metabolic responses to biofuel ethanol in cyanobacterial Synechocystis sp. PCC 6803. J Proteome Res 2012, 11:5286-5300.
• [28]Qiao J, Shao M, Chen L, Wang J, Wu G, Tian X, Liu J, Huang S, Zhang W: Systematic characterization of hypothetical proteins in Synechocystis sp. PCC 6803 reveals proteins functionally relevant to stress responses. Gene 2013, 512:6-15.
• [29]Zhu H, Ren X, Wang J, Song Z, Shi M, Qiao J, Tian X, Liu J, Chen L, Zhang W: Integrated OMICS guided engineering of biofuel butanol-tolerance in photosynthetic Synechocystis sp. PCC 6803. Biotechnol Biofuels 2013, 6:106. BioMed Central Full Text
• [30]Salis H, Tamsir A, Voigt C: Engineering bacterial signals and sensors. Contrib Microbiol 2009, 16:194-225.
• [31]Ashby MK, Houmard J: Cyanobacterial two-component proteins: structure, diversity, distribution, and evolution. Microbiol Mol Biol Rev 2006, 70:472-509.
• [32]Shoumskaya MA, Paithoonrangsarid K, Kanesaki Y, Los DA, Zinchenko VV, Tanticharoen M, Suzuki I, Murata N: Identical Hik-Rre systems are involved in perception and transduction of salt signals and hyperosmotic signals but regulate the expression of individual genes to different extents in Synechocystis. J Biol Chem 2005, 280:21531-21538.
• [33]Sato S, Shimoda Y, Muraki A, Kohara M, Nakamura Y, Tabata S: A large-scale protein protein interaction analysis in Synechocystis sp. PCC6803. DNA Res 2007, 14:207-216.
• [34]Chen Y, Zhang J, Luo J, Tu JM, Zeng XL, Xie J, Zhou M, Zhao JQ, Scheer H, Zhao KH: Photophysical diversity of two novel cyanobacteriochromes with phycocyanobilin chromophores: photochemistry and dark reversion kinetics. FEBS J 2012, 279:40-54.
• [35]Kaneko T, Nakamura Y, Sasamoto S, Watanabe A, Kohara M, Matsumoto M, Shimpo S, Yamada M, Tabata S: Structural analysis of four large plasmids harboring in a unicellular cyanobacterium, Synechocystis sp. PCC 6803. DNA Res 2003, 10:221-228.
• [36]Ermakova-Gerdes S, Vermaas W: Inactivation of the open reading frame slr0399 in Synechocystissp. PCC 6803 functionally complements mutations near the Q(A) niche of photosystem II. A possible role of Slr0399 as a chaperone for quinone binding. J Biol Chem 1999, 274:30540-30549.
• [37]Alvey RM, Biswas A, Schluchter WM, Bryant DA: Attachment of noncognate chromophores to CpcA of Synechocystis sp. PCC 6803 and Synechococcus sp. PCC 7002 by heterologous expression in Escherichia coli. Biochemistry 2011, 50:4890-4902.
• [38]Mazouni K, Domain F, Chauvat F, Cassier-Chauvat C: Expression and regulation of the crucial plant-like ferredoxin of cyanobacteria. Mol Microbiol 2003, 49:1019-1029.
• [39]Walters EM, Garcia-Serres R, Naik SG, Bourquin F, Glauser DA, Schurmann P, Huynh BH, Johnson MK: Role of histidine-86 in the catalytic mechanism of ferredoxin:thioredoxin reductase. Biochemistry 2009, 48:1016-1024.
• [40]Perez-Perez ME, Martin-Figueroa E, Florencio FJ: Photosynthetic regulation of the cyanobacterium Synechocystis sp. PCC 6803 thioredoxin system and functional analysis of TrxB (Trx x) and TrxQ (Trx y) thioredoxins. Mol Plant 2009, 2:270-283.
• [41]Shen JR, Vermaas W, Inoue Y: The role of cytochrome c-550 as studied through reverse genetics and mutant characterization in Synechocystis sp. PCC 6803. J Biol Chem 1995, 270:6901-6907.
• [42]Nodop A, Pietsch D, Hocker R, Becker A, Pistorius EK, Forchhammer K, Michel KP: Transcript profiling reveals new insights into the acclimation of the mesophilic fresh-water cyanobacterium Synechococcus elongatus PCC 7942 to iron starvation. Plant Physiol 2008, 147:747-763.
• [43]Ni Y, Song L, Qian X, Sun Z: Proteomic analysis of Pseudomonas putida reveals an organic solvent tolerance-related gene mmsB. PLoS One 2013, 8:e55858.
• [44]Li M, Yang Q, Gao Y, Wu Q: N-terminus deletion affecting the preparation of soluble cyanobacterial glutaredoxin in Escherichia coli. Biochemistry (Mosc) 2007, 72:313-319.
• [45]Lopez-Maury L, Sanchez-Riego AM, Reyes JC, Florencio FJ: The glutathione/glutaredoxin system is essential for arsenate reduction in Synechocystis sp. strain PCC 6803. J Bacteriol 2009, 191:3534-3543.
• [46]Thorsteinsson MV, Bevan DR, Potts M, Dou Y, Eich RF, Hargrove MS, Gibson QH, Olson JS: A cyanobacterial hemoglobin with unusual ligand binding kinetics and stability properties. Biochemistry 1999, 38:2117-2126.
• [47]Hagemann M: Molecular biology of cyanobacterial salt acclimation. FEMS Microbiol Rev 2011, 35:87-123.
• [48]Hanaoka M, Takai N, Hosokawa N, Fujiwara M, Akimoto Y, Kobori N, Iwasaki H, Kondo T, Tanaka K: RpaB, another response regulator operating circadian clock-dependent transcriptional regulation in Synechococcus elongatus PCC 7942. J Biol Chem 2012, 287:26321-26327.
• [49]Yang S, Land ML, Klingeman DM, Pelletier DA, Lu TY, Martin SL, Guo HB, Smith JC, Brown SD: Paradigm for industrial strain improvement identifies sodium acetate tolerance loci in Zymomonas mobilis and Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 2010, 107:10395-10400.
• [50]Black K, Buikema WJ, Haselkorn R: The hglK gene is required for localization of heterocyst-specific glycolipids in the cyanobacterium Anabaena sp. strain PCC 7120. J Bacteriol 1995, 177:6440-6448.
• [51]Merino-Puerto V, Mariscal V, Mullineaux CW, Herrero A, Flores E: Fra proteins influencing filament integrity, diazotrophy and localization of septal protein SepJ in the heterocyst-forming cyanobacterium Anabaena sp. Mol Microbiol 2010, 75:1159-1170.
• [52]Ding J, Huang X, Zhang L, Zhao N, Yang D, Zhang K: Tolerance and stress response to ethanol in the yeast Saccharomyces cerevisiae. Appl Microbiol Biotechnol 2009, 85:253-263.
• [53]Shibata M, Ohkawa H, Kaneko T, Fukuzawa H, Tabata S, Kaplan A, Ogawa T: Distinct constitutive and low-CO2-induced CO2 uptake systems in cyanobacteria: genes involved and their phylogenetic relationship with homologous genes in other organisms. Proc Natl Acad Sci U S A 2001, 98:11789-11794.
• [54]Hisbergues M, Gaitatzes CG, Joset F, Bedu S, Smith TF: A noncanonical WD-repeat protein from the cyanobacterium Synechocystis PCC6803: structural and functional study. Protein Sci 2001, 10:293-300.
• [55]Zhang Z, Pendse ND, Phillips KN, Cotner JB, Khodursky A: Gene expression patterns of sulfur starvation in Synechocystis sp. PCC 6803. BMC Genomics 2008, 9:344. BioMed Central Full Text
• [56]Fuszard MA, Ow SY, Gan CS, Noirel J, Ternan NG, McMullan G, Biggs CA, Reardon KF, Wright PC: The quantitative proteomic response of Synechocystis sp. PCC6803 to phosphate acclimation. Aquat Biosyst 2013, 9:5. BioMed Central Full Text
• [57]Wilde A, Churin Y, Schubert H, Borner T: Disruption of a Synechocystis sp. PCC 6803 gene with partial similarity to phytochrome genes alters growth under changing light qualities. FEBS Lett 1997, 406:89-92.
• [58]Pollari M, Gunnelius L, Tuominen I, Ruotsalainen V, Tyystjarvi E, Salminen T, Tyystjarvi T: Characterization of single and double inactivation strains reveals new physiological roles for group 2 sigma factors in the cyanobacterium Synechocystis sp. PCC 6803. Plant Physiol 2008, 147:1994-2005.
• [59]Lawrence CE, Altschul SF, Boguski MS, Liu JS, Neuwald AF, Wootton JC: Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science 1993, 262:208-214.
• [60]Thompson W, Rouchka EC, Lawrence CE: Gibbs Recursive Sampler: finding transcription factor binding sites. Nucleic Acids Res 2003, 31:3580-3585.
• [61]van Helden J: Regulatory sequence analysis tools. Nucleic Acids Res 2003, 31:3593-3596.
• [62]Crooks GE, Hon G, Chandonia JM, Brenner SE: WebLogo: a sequence logo generator. Genome Res 2004, 14:1188-1190.
• [63]Vuilleumier S: Bacterial glutathione S-transferases: what are they good for? J Bacteriol 1997, 179:1431-1441.
• [64]Cameron JC, Pakrasi HB: Glutathione in Synechocystis 6803: a closer look into the physiology of a ∆gshB mutant. Plant Signal Behav 2011, 6:89-92.
• [65]Wang HL, Postier BL, Burnap RL: Optimization of fusion PCR for in vitro construction of gene knockout fragments. Biotechniques 2002, 33:26-30.
• [66]Kloft N, Rasch G, Forchhammer K: Protein phosphatase PphA from Synechocystis sp. PCC 6803: the physiological framework of PII-P dephosphorylation. Microbiology 2005, 151:1275-1283.