Integrated OMICS guided engineering of biofuel butanol-tolerance in photosynthetic Synechocystis sp. PCC 6803

Biotechnology for Biofuels

Volumn 6, Issue 1, 2013, Pages

  Zhu, Hongji ^a,b   Ren, Xiaoyue ^a,b   Wang, Jiangxin ^a,b   Song, Zhongdi ^a,b   Shi, Mengliang ^a,b   Qiao, Jianjun ^a,b   Tian, Xiaoxu ^a,b   Liu, Jie ^a,b   Chen, Lei ^a,b   Zhang, Weiwen ^a,b  

^a TIANJIN UNIVERSITY   (China)

^b BEIJING UNIVERSITY OF POSTS AND TELECOMMUNICATIONS   (China)

Author keywords

Butanol; Metabolomics; Synechocystis; Tolerance; Transcriptomics

Indexed keywords

CYANOBACTERIUM SYNECHOCYSTIS; METABOLOMICS; MOLECULAR MECHANISM; PHENOTYPIC ANALYSIS; STRESS-RELATED PROTEINS; SYNECHOCYSTIS; SYNECHOCYSTIS SP. PCC 6803; TRANSCRIPTOMICS;

AMINO ACIDS; BUTENES; FITS AND TOLERANCES; GENETIC ENGINEERING; PROTEINS; UREA;

GENES;

BIOFUEL; CYANOBACTERIUM; EXPERIMENTAL STUDY; GENE EXPRESSION; MOLECULAR ANALYSIS; PHOTOSYNTHESIS; RNA; TOLERANCE;

CYANOBACTERIA; SYNECHOCYSTIS; SYNECHOCYSTIS SP.; SYNECHOCYSTIS SP. PCC 6803;

EID: 84880893189     PISSN: 17546834     EISSN: None     Source Type: Journal    
DOI: 10.1186/1754-6834-6-106     Document Type: Article

References (69)

1. Biobutanol: an attractive biofuel. Durre P, Biotechnol J 2007 2 1525 1534 10.1002/biot.200700168 17924389
2. Fermentative butanol production: bulk chemical and biofuel. Durre P, Ann NY Acad Sci 2008 1125 353 362 10.1196/annals.1419.009 18378605 (Pubitemid 351451155)
3. Solventogenic enzymes of Clostridium acetobutylicum: catalytic properties, genetic organization, and transcriptional regulation. Durre P, Fischer RJ, Kuhn A, Lorenz K, Schreiber W, Sturzenhofecker B, Ullmann S, Winzer K, Sauer U, FEMS Microbiol Rev 1995 17 251 262 7576767
4. Fermentative butanol production by Clostridia. Lee SY, Park JH, Jang SH, Nielsen LK, Kim J, Jung KS, Biotechnol Bioeng 2008 101 209 228 10.1002/bit.22003 18727018
5. Acetone-butanol-ethanol production from concentrated substrate: reduction in substrate inhibition by fed-batch technique and product inhibition by gas stripping. Ezeji TC, Qureshi N, Blaschek H, Appl Micriobiol Biotechnol 2004 63 653 658 10.1007/s00253-003-1400-x (Pubitemid 38316691)
6. Butanol fermentation research: upstream and downstream manipulations. Ezeji TC, Qureshi N, Blaschek HP, Chem Rec 2004 4 305 314 10.1002/tcr.20023 15543610 (Pubitemid 40012824)
7. Problems with the microbial production of butanol. Zheng YN, Li LZ, Xian M, Ma YJ, Yang JM, Xu X, He DZ, J Ind Microbiol Biotechnol 2009 36 1127 1138 10.1007/s10295-009-0609-9 19562394
8. Metabolic engineering of Clostridium acetobutylicum: recent advances to improve butanol production. Lutke-Eversloh T, Bahl H, Curr Opin Biotechnol 2011 22 634 647 10.1016/j.copbio.2011.01.011 21377350
9. Improving photosynthetic efficiency for greater yield. Zhu XG, Long SP, Ort DR, Annu Rev Plant Biol 2010 61 235 261 10.1146/annurev-arplant-042809- 112206 20192734
10. Cyanobacterial biofuel production. Machado IM, Atsumi S, J Biotechnol 2012 162 50 56 10.1016/j.jbiotec.2012.03.005 22446641
11. Direct photosynthetic recycling of carbon dioxide to isobutyraldehyde. Atsumi S, Higashide W, Liao J, Nat Biotechnol 2009 27 1177 1180 10.1038/nbt.1586 19915552
12. Metabolic engineering of cyanobacteria for 1-butanol production from carbon dioxide. Lan E, Liao J, Metab Eng 2011 13 353 363 10.1016/j.ymben.2011. 04.004 21569861
13. Metabolic engineering of Escherichia coli for 1-butanol production. Atsumi S, Cann AF, Connor MR, Shen CR, Smith KM, Brynildsen MP, Chou KJ, Hanai T, Liao JC, Metab Eng 2008 10 305 311 10.1016/j.ymben.2007.08.003 17942358
14. Expression of Clostridium acetobutylicum butanol synthetic genes in Escherichia coli. Inui M, Suda M, Kimura S, Yasuda K, Suzuki H, Toda H, Yamamoto S, Okino S, Suzuki N, Yukawa H, Appl Microbiol Biotechnol 2008 77 1305 1316 10.1007/s00253-007-1257-5 18060402
15. Metabolic engineering of Escherichia coli for 1-butanol and 1-propanol production via the keto-acid pathways. Shen CR, Liao JC, Metab Eng 2008 10 312 320 10.1016/j.ymben.2008.08.001 18775501
16. A comparative view of metabolite and substrate stress and tolerance in microbial bioprocessing: From biofuels and chemicals, to biocatalysis and bioremediation. Nicolaou SA, Gaida SM, Papoutsakis ET, Metab Eng 2010 12 307 331 10.1016/j.ymben.2010.03.004 20346409
17. Engineering microbes for tolerance to next-generation biofuels. Dunlop MJ, Biotechnol Biofuels 2011 4 32 10.1186/1754-6834-4-32 21936941
18. Engineering solventogenic clostridia. Papoutsakis ET, Curr Opin Biotechnol 2008 19 420 429 10.1016/j.copbio.2008.08.003 18760360
19. Achievements and perspectives to overcome the poor solvent resistance in acetone and butanol-producing microorganisms. Ezeji T, Milne C, Price ND, Blaschek HP, Appl Microbiol Biotechnol 2010 85 1697 1712 10.1007/s00253-009- 2390-0 20033401
20. Butanol tolerance of Clostridium beijerinckii NCIMB 8052 associated with down-regulation of gldA by antisense RNA. Liyanage H, Young M, Kashket ER, J Mol Microbiol Biotechnol 2000 2 87 93 10937492 (Pubitemid 30125165)
21. Identification and Characterization of two functionally unknown genes involved in butanol tolerance of Clostridium acetobutylicum. Jia K, Zhang Y, Li Y, PLoS One 2012 7 38815 10.1371/journal.pone.0038815 22768047
22. Engineering global transcription factor cyclic AMP receptor protein of Escherichia coli for improved 1-butanol tolerance. Zhang H, Chong H, Ching CB, Song H, Jiang R, Appl Microbiol Biotechnol 2012 94 1107 1117 10.1007/s00253-012-4012-5 22466954
23. Evolution, genomic analysis, and reconstruction of isobutanol tolerance in Escherichia coli. Atsumi S, Wu TY, Machado IMP, Huang WC, Chen PY, Pellegrini M, Liao JC, Mol Syst Biol 2010 6 449 21179021
24. Genomic library screens for genes involved in n-butanol tolerance in Escherichia coli. Reyes LH, Almario MP, Kao KC, PLoS One 2011 6 3 17678 10.1371/journal.pone.0017678 21408113
25. Integrating multiple 'omics' analysis for microbial biology: application and methodologies. Zhang W, Li F, Nie L, Microbiology 2010 156 287 301 10.1099/mic.0.034793-0 19910409
26. Quantitative proteomics reveals dynamic responses of Synechocystis sp. PCC 6803 to next-generation biofuel butanol. Tian XX, Chen L, Wang JX, Qiao J, Zhang WW, J Proteomics 2012 78 326 345 23079071
27. Structural analysis of four large plasmids harboring in a unicellular cyanobacterium, Synechocystis sp. PCC 6803. Kaneko T, Nakamura Y, Sasamoto S, Watanabe A, Kohara M, Matsumoto M, Shimpo S, Yamada M, Tabata S, DNA Res 2003 10 221 228 10.1093/dnares/10.5.221 14686584 (Pubitemid 37493724)
28. YkdA and YvtA, HtrA-like serine proteases in Bacillus subtilis, engage in negative autoregulation and reciprocal cross-regulation of ykdA and yvtA gene expression. Noone D, Howell A, Collery R, Devine KM, J Bacteriol 2001 183 654 663 10.1128/JB.183.2.654-663.2001 11133960 (Pubitemid 32048125)
29. Formation of a distinctive complex between the inducible bacterial lysine decarboxylase and a novel AAA + ATPase. Snider J, Gutsche I, Lin M, Baby S, Cox B, Butland G, Greenblatt J, Emili A, Houry WA, J Biol Chem 2006 281 1532 1546 16301313
30. Identification of a putative chaperone involved in stress resistance and virulence in Francisella tularensis. Dieppedale J, Sobral D, Dupuis M, Dubail I, Klimentova J, Stulik J, Postic G, Frapy E, Meibom KL, Barel M, Charbit A, Infect Immun 2011 79 1428 1439 10.1128/IAI.01012-10 21245269
31. Functional genomic study of exogenous n-butanol stress in Escherichia coli. Rutherford BJ, Dahl RH, Price RE, Szmidt HL, Benke PI, Mukhopadhyay A, Keasling JD, Appl Environ Microbiol 2010 76 1935 1945 10.1128/AEM.02323-09 20118358
32. Role of bacterioferritin comigratory protein and glutathione peroxidase-reductase system in promoting bentazone tolerance in a mutant of Synechococcus elongatus PCC7942. Das PK, Bagchi SN, Protoplasma 2012 249 65 74 10.1007/s00709-011-0262-9 21267607
33. Stress-dependent regulation of a monothiol glutaredoxin gene from Schizosaccharomyces pombe. Kim HG, Kim BC, Park EH, Lim CJ, Can J Microbiol 2005 51 613 620 10.1139/w05-034 16175211 (Pubitemid 41719745)
34. Glutaredoxins Grx4 and Grx3 of Saccharomyces cerevisiae play a role in actin dynamics through their Trx domains, which contributes to oxidative stress resistance. Pujol-Carrion N, De la Torre-Ruiz MA A, Appl Environ Microbiol 2010 76 7826 7835 10.1128/AEM.01755-10 20889785
35. Quantitative iTRAQ LC-MS/MS proteomics reveals metabolic response to biofuel ethanol in cyanobacterial Synechocystis sp. PCC 6803. Qiao JJ, Wang JX, Chen L, Tian XX, Zhang WW, J Proteome Res 2012 11 11 5286 5300 10.1021/pr300504w 23062023
36. Oxidative stress and heat-shock responses in Desulfovibrio vulgaris by genome-wide transcriptomic analysis. Zhang W, Culley DE, Hogan M, Vitirit L, Brockman FJ, Antonie Van Leeuwenhoek 2006 90 41 55 10.1007/s10482-006-9059-9 16680520 (Pubitemid 44056924)
37. The yeast peptide-methionine sulfoxide reductase functions as an antioxidant in vivo. Moskovitz J, Berlett B, Poston JM, Stadtman ER, Proc Natl Acad Sci USA 1997 94 9585 9589 10.1073/pnas.94.18.9585 9275166 (Pubitemid 27408105)
38. Over-expression of peptide-methionine sulfoxide reductase in Saccharomyces cerevisiae and human T cells provides them with high resistance to oxidative stress. Moskovitz J, Lescher E, Berlett BS, Azare J, Poston JM, Stadtman ER, Proc Natl Acad Sci USA 1998 95 14071 14075 10.1073/pnas.95.24.14071 9826655 (Pubitemid 28549322)
39. Posttranslational modification influences the effects of MgrA on norA expression in Staphylococcus aureus. Truong-Bolduc QC, Ding Y, Hooper DC, J Bacteriol 2008 190 7375 7381 10.1128/JB.01068-08 18805983
40. Bacterial protein translocase: a unique molecular machine with an army of substrates. Economou A, FEBS Lett 2000 476 18 21 10.1016/S0014-5793(00)01662-8 10878242 (Pubitemid 30394642)
41. Evidence for a dynamic and transient pathway through the TAT protein transport machinery. Cline K, McCaffery M, EMBO J 2007 26 3039 3049 10.1038/sj.emboj.7601759 17568769 (Pubitemid 47057499)
42. Concerted changes in gene expression and Cell physiology of the cyanobacterium Synechocystis sp. Strain PCC 6803 during transitions between nitrogen and light-limited growth. von Wobeser E, Ibelings BW, Bok J, Krasikov V, Huisman J, Matthijs HCP, Plant Physiol 2011 155 1445 1457 10.1104/pp.110.165837 21205618
43. Ecological and agricultural significance of bacterial polyhydroxyalkanoates. Kadouri D, Jurkevitch E, Okon Y, Castro-Sowinski S, Crit Rev Microbiol 2005 31 55 67 10.1080/10408410590899228 15986831 (Pubitemid 40756858)
44. Effect of nitrogen source on cyanophycin synthesis in Synechocystis sp. strain PCC 6308. Kolodny NH, Bauer D, Bryce K, Klucevsek K, Lane A, Medeiros L, Mercer W, Moin S, Park D, Petersen J, Wright J, Yuen C, Wolfson AJ, Allen MM, J Bacteriol 2006 188 934 940 10.1128/JB.188.3.934-940.2006 16428397 (Pubitemid 43146409)
45. Coordinate up-regulation of carotenoid biosynthesis as a response to light stress in Synechococcus PCC7942. Schäfer L, Sandmann M, Woitsch S, Sandmann G, Plant Cell Environ 2006 29 1349 1356 10.1111/j.1365-3040.2006.01515. x 17080956 (Pubitemid 43855751)
46. Enhancement of carotenoids by mutation and stress induced carotenogenic genes in Haematococcus pluvialis mutants. Sandesh Kamath B, Vidhyavathi R, Sarada R, Ravishankar GA, Bioresour Technol 2008 99 8667 8673 10.1016/j.biortech.2008.04.013 18499448
47. Transcript profiling reveals new insights into the acclimation of the mesophilic fresh-water cyanobacterium Synechococcus elongatus PCC 7942 to iron starvation. Nodop A, Pietsch D, Höcker R, Becker A, Pistorius EK, Forchhammer K, Michel KP, Plant Physiol 2008 147 747 763 10.1104/pp.107.114058 18424627 (Pubitemid 352844321)
48. Proteomics combines morphological, physiological and biochemical attributes to unravel the survival strategy of Anabaena sp. PCC7120 under arsenic stress. Pandey S, Rai R, Rai LC, J Proteomics 2012 75 921 937 10.1016/j.jprot.2011.10.011 22057044
49. Assessment of salinity-induced photorespiratory glycolate metabolism in Anabaena sp. PCC 7120. Srivastava AK, Alexova R, Jeon YJ, Kohli GS, Neilan BA, Microbiology 2011 157 911 917 10.1099/mic.0.045682-0 21163840
50. Global proteomics reveal an atypical strategy for carbon/nitrogen assimilation by a cyanobacterium under diverse environmental perturbations. Wegener KM, Singh AK, Jacobs JM, Elvitigala T, Welsh EA, Keren N, Gritsenko MA, Ghosh BK, Camp DG 2nd, Smith RD, Pakrasi HB, Mol Cell Proteomics 2010 9 2678 2689 10.1074/mcp.M110.000109 20858728
51. Arginine catabolism in the cyanobacterium Synechocystis sp. Strain PCC 6803 involves the urea cycle and arginase pathway. Quintero MJ, Muro-Pastor AM, Herrero A, Flores E, J Bacteriol 2000 182 1008 1015 10.1128/JB.182.4.1008-1015. 2000 10648527 (Pubitemid 30075024)
52. Parallel analysis of transcript and metabolic profiles: a new approach in systems biology. Urbanczyk-Wochniak E, Luedemann A, Kopka J, Selbig J, Roessner-Tunali U, Willmitzer L, Fernie AR, EMBO Rep 2003 4 989 993 10.1038/sj.embor.embor944 12973302 (Pubitemid 37407468)
53. Integrating profiling data: using linear correlation to reveal coregulation of transcript and metabolites. Urbanczyk-Wochniak E, Willmitzer L, Fernie AR, Methods Mol Biol 2007 358 77 85 10.1007/978-1-59745-244-1-5 17035681
54. An integrated genomics approach to define niche establishment by Rhodococcus fascians. Depuydt S, Trenkamp S, Fernie AR, Elftieh S, Renou JP, Vuylsteke M, Holsters M, Vereecke D, Plant Physiol 2009 149 1366 1386 10.1104/pp.108.131805 19118125
55. Transcriptomic and metabolomic profiling of Zymomonas mobilis during aerobic and anaerobic fermentations. Yang S, Tschaplinski TJ, Engle NL, Carroll SL, Martin SL, Davison BH, Palumbo AV, Rodriguez M Jr, Brown SD, BMC Genomics 2009 10 34 10.1186/1471-2164-10-34 19154596
56. Proteomic analysis of a penicillin-tolerant rgg mutant strain of Streptococcus pyogenes. Chaussee MA, McDowell EJ, Rieck LD, Callegari EA, Chaussee MS, J Antimicrob Chemother 2006 58 752 759 10.1093/jac/dkl319 16891633 (Pubitemid 44390948)
57. Development of quinoxaline 1, 4-dioxides resistance in Escherichia coli and molecular change under resistance selection. Guo W, Hao H, Dai M, Wang Y, Huang L, Peng D, Wang X, Wang H, Yao M, Sun Y, Liu Z, Yuan Z, PLoS One 2012 7 43322 10.1371/journal.pone.0043322 22952665
58. Analysis of metabolic pathways and fluxes in a newly discovered thermophilic and ethanol-tolerant Geobacillus strain. Tang YJ, Sapra R, Joyner D, Hazen TC, Myers S, Reichmuth D, Blanch H, Keasling JD, Biotechnol Bioeng 2009 102 1377 1386 10.1002/bit.22181 19016470
59. Localization and function of the IdiA homologue Slr1295 in the cyanobacterium Synechocystis sp. strain PCC 6803. Tölle J, Michel KP, Kruip J, Kahmann U, Preisfeld A, Pistorius EK, Microbiology 2002 148 3293 3305 12368463 (Pubitemid 35243729)
60. Proteomic screening of salt-stress-induced changes in plasma membranes of Synechocystis sp. strain PCC 6803. Huang F, Fulda S, Hagemann M, Norling B, Proteomics 2006 6 910 920 10.1002/pmic.200500114 16400685 (Pubitemid 43260215)
61. Cyanobacterial ycf27 gene products regulate energy transfer from phycobilisomes to photosystems I and II. Ashby MK, Mullineaux CW, FEMS Microbiol Lett 1999 181 253 260 10.1111/j.1574-6968.1999.tb08852.x 10585546
62. Integrative analysis of transcriptomic and proteomic data: challenges, solutions and applications. Nie L, Wu G, Culley DE, Scholten JC, Zhang W, Crit Rev Biotechnol 2007 27 63 75 10.1080/07388550701334212 17578703 (Pubitemid 46956894)
63. Differential expression analysis for sequence count data. Anders S, Huber W, Genome Biol 2010 11 106 10.1186/gb-2010-11-10-r106 20979621
64. Protein phosphatase PphA from Synechocystis sp. PCC 6803: the physiological framework of PII-P dephosphorylation. Kloft N, Rasch G, Forchhammer K, Microbiology 2005 151 1275 1283 10.1099/mic.0.27771-0 15817794 (Pubitemid 40568022)
65. Metabolic profiling allows comprehensive phenotyping of genetically or environmentally modified plant systems. Roessner U, Luedemann A, Brust D, Fiehn O, Linke T, Willmitzer L, Fernie A, Plant Cell 2001 13 11 29 11158526 (Pubitemid 32177030)
66. An integrated method for spectrum extraction and compound identification from GC/MS data. Stein SE, Mass Spectrom 1999 10 8 770 781 (Pubitemid 34506228)
67. Metabolomics-the link between genotypes and phenotypes. Fiehn O, Plant Mol Biol 2002 48 155 171 10.1023/A:1013713905833 11860207 (Pubitemid 34128498)
68. Metabolomic analysis in severe childhood pneumonia in the Gambia, West Africa: findings from a pilot study. Laiakis EC, Morris GA, Fornace AJ, Howie SR, PLoS One 2010 5 9 12655 10.1371/journal.pone.0012655 20844590
69. Optimization of fusion PCR for in vitro construction of gene knockout fragments. Wang HL, Postier BL, Burnap RL, Biotechniques 2002 33 26 28 30