CIESC Journal ›› 2015, Vol. 66 ›› Issue (10): 3811-2819.DOI: 10.11949/j.issn.0438-1157.20150935
Previous Articles Next Articles
ZHAO Yujia, ZHANG Genlin, ZHOU Xiaohong, LI Chun
Received:
2015-06-16
Revised:
2015-07-16
Online:
2015-10-05
Published:
2015-10-05
Supported by:
supported by the National Science Fund for Distinguished Young Scholars(21425624)and the National Natural Science Foundation of China(21376028, 21476026).
赵雨佳, 张根林, 周晓宏, 李春
通讯作者:
李春
基金资助:
国家杰出青年科学基金项目(21425624);国家自然科学基金面上项目(21376028,21476026)。
CLC Number:
ZHAO Yujia, ZHANG Genlin, ZHOU Xiaohong, LI Chun. Intelligent and fine regulation of microbial cell factory based on riboswitches[J]. CIESC Journal, 2015, 66(10): 3811-2819.
赵雨佳, 张根林, 周晓宏, 李春. 核糖核酸开关用于微生物细胞工厂的智能与精细调控[J]. 化工学报, 2015, 66(10): 3811-2819.
[1] | Lai Shujuan, Zhang Yun, Liu Shuwen, Liang Yong, Shang Xiuling, Chai Xin, Wen Tingyi. Metabolic engineering and flux analysis of Corynebacterium glutamicum for L-serine production [J]. Science China Life Sciences, 2012, 55(4): 283-290. |
[2] | Wu Y, Li P, Zheng P, Zhou W, Chen N, Sun J. Complete genome sequence of Corynebacterium glutamicum B253, a Chinese lysine-producing strain [J]. J. Biotechnol., 2015, 4(207): 10-11. |
[3] | Wang N, Ni Y, Shi F. Deletion of odhA or pyc improves production of γ-aminobutyric acid and its precursor L-glutamate in recombinant Corynebacterium glutamicum [J]. Biotechnol. Lett., 2015, 37(7): 1473-1481. |
[4] | Shi X, Chen Y, Ren H, Liu D, Zhao T, Zhao N, Ying H. Economically enhanced succinic acid fermentation from cassava bagasse hydrolysate using Corynebacterium glutamicum immobilized in porous polyurethane filler [J]. Bioresour. Technol., 2014, 174: 190-197. |
[5] | Dae-Kyun Ro, Eric M Paradise, Jay D Keasling, et al. Production of the antimalarial drug precursor artemisinic acid in engineered yeast [J]. Nature, 2005, 440(7086): 940-943. |
[6] | Patrick J Westfall, Douglas J Pitera, Jay D Keasling, et al. Production of amorphadiene in yeast, and its conversion to dihydroartemisinic acid, precursor to the antimalarial agent artemisinin [J]. Proc. Natl. Acad. Sci. USA, 2012, 109(3): E111-E118. |
[7] | Jennewein S, Park H, DeJong J M, Long R M, Bollon A P, Croteau R B. Coexpression in yeast of Taxus cytochrome P450 reductase with cytochrome P450 oxygenases involved in Taxol biosynthesis [J]. Biotechnol. Bioeng., 2005, 89(5): 588-598. |
[8] | Guo J, Zhou Y J, Hillwig M L, Huang L, et al. CYP76AH1 catalyzes turnover of miltiradiene in tanshinones biosynthesis and enables heterologous production of ferruginol in yeasts [J]. Proc. Natl. Acad. Sci. USA, 2013, 110(29): 12108-12113. |
[9] | Gao Z X, Zhao H, Li Z M, Tan X M, Lu X F. Photosynthetic production of ethanol from carbon dioxide in genetically engineered cyanobacteria [J]. Energy & Environmental Science, 2012, 5(12): 9857-9865. |
[10] | Lan E I, Liao J C. Metabolic engineering of cyanobacteria for 1-butanol production from carbon dioxide [J]. Metabolic Engineering, 2011, 13(4): 353-363. |
[11] | Meng D C, Wang Y, Wu L P, Shen R, Chen J C, Wu Q, Chen G Q. Production of poly (3-hydroxypropionate) and poly (3-hydroxybutyrate-co-3-hydroxypropionate) from glucose by engineering Escherichia coli [J]. Metab. Eng., 2015, 29: 189-195. |
[12] | Jari M, Khatami S R, Galehdari H, Shafiei M. Cloning and expression of poly 3-hydroxybutyrate operon into Escherichia coli [J]. Jundishapur Journal of Microbiology, 2015, 8(2): e16318. |
[13] | Nahvi A, Sudarsan N, Ebert M S, Zou X, Brown K L, Breaker R R. Genetic control by a metabolite binding mRNA [J]. ChemBiol., 2002, 9(9): 1043. |
[14] | Winkler W C, Cohen-Chalamish S, Breaker R R. An mRNA structure that controls gene expression by binding FMN [J]. Proc. Natl. Acad. Sci. USA, 2002, 99: 15908-15913. |
[15] | Mironov A S, Gusarov I, Rafikov R, Lopez L E, Shatalin K, Kreneva R A, Perumov D A, Nudler E. Sensing small molecules by nascent RNA: a mechanism to control transcription in bacteria [J]. Cell, 2002, 111: 747-756. |
[16] | Breaker R R. Prospects for riboswitch discovery and analysis [J]. Molecular Cell, 2011, 43(6): 867-879. |
[17] | Dann C E 3rd, Wakeman C A, Sieling C L, Baker S C, Irnov I, Winkler W C. Structure and mechanism of a metal-sensing regulatory RNA [J]. Cell, 2007, 130(5): 878-892. |
[18] | Ramesh A, Winkler W C. Magnesium-sensing riboswitches in bacteria [J]. Journal of RNA Biol., 2010, 7: 77-83. |
[19] | Chawla M, Credendino R, Poater A, Oliva R, Cavallo L. Structural stability, acidity, and halide selectivity of the fluoride riboswitch recognition site [J]. J. Am. Chem. Soc., 2015, 137(1): 299-306. |
[20] | Furukawa K, Ramesh A, Zhou Z Y, Weinberg Z, Vallery T, Wade W C, Breaker R R. Bacterial riboswitches cooperatively bind Ni2+ or Co2+ ions and control expression of heavy metal transporters [J]. Molecular Cell, 2015, 57(6): 1088-1098. |
[21] | McCown P J, Winkler W C, Breaker R R. Mechanism and distribution of glmS ribozymes [J]. Methods. Mol. Biol., 2012, 848: 113-129. |
[22] | Soukup J K. The structural and functional uniqueness of the glmS ribozyme [J]. Catalytic Rna., 2013, 120: 173-193. |
[23] | Mandal M, Lee M, Barrick J E, Weinberg Z, Emilsson G M, Ruzzo W L, Breaker R R. A glycine-dependent riboswitch that uses cooperative binding to control gene expression. [J]. Science, 2004, 306(5694): 275-279. |
[24] | Mellin J R, Pascale Cossart. Unexpected versatility in bacterial riboswitches [J]. Trends in Genetics, 2015, 31(3): 150-156. |
[25] | Wilson-Mitchell S N, Grundy F J, Henkin T M. Analysis of lysine recognition and specificity of the Bacillus subtilis L box riboswitch [J]. Nucleic Acids Res., 2012, 40(12): 5706-5717. |
[26] | Furukawa K, Gu H, Sudarsan N, Hayakawa Y, Hyodo M, Breaker R R. Identification of ligand analogues that control c-di-GMP riboswitches [J]. ACS Chem. Biol., 2012, 7(8): 1436-1443. |
[27] | Sudarsan N, Lee E R, Weinberg Z, Moy R H, Kim J N, Link K H, Breaker R R. Riboswitches in eubacteria sense the second messenger cyclic di-GMP [J]. Science, 2008, 321: 411-413. |
[28] | Lee E R, Baker J L, Weinberg Z, Sudarsan N, Breaker R. An allosteric self-splicing ribozyme triggered by a bacterial second messenger [J]. Science, 2010, 329(5993): 845-848. |
[29] | Wachsmuth M, Findeiss S, Weissheimer N, Stadler P F, Mörl M. De novo design of a synthetic riboswitch that regulates transcription termination [J]. Nucleic Acids Res., 2013, 41(4): 2541-2551. |
[30] | Desai S K, Gallivan J P. Genetic screens and selections for small molecules based on a synthetic riboswitch that activates protein translation [J]. Journal of the American Chemical Society, 2004, 126(41): 13247-13254. |
[31] | Tang J, Breaker R R. Rational design of allosteric ribozymes [J]. Chemistry & Biology, 1997, 4(6): 453-459. |
[32] | Zhou L B, Zeng A P. Exploring lysine riboswitch for metabolic flux control and improvement of L-lysine synthesis in Corynebacterium glutamicum [J]. ACS Synth. Biol., 2015, 4(6): 729-734. |
[33] | Yang J, Seo S W, Jang S, Shin S I, Lim C H, Roh T Y, Jung G Y. Synthetic RNA devices to expedite the evolution of metabolite-producing microbes [J]. Nat. Commun., 2013, 4: 1413. |
[34] | Muranaka N, Sharma V, Nomura Y, Yokobayashi Y. An efficient platform for genetic selection and screening of gene switches in Escherichia coli [J]. Nucleic Acids Res., 2009, 37(5): e39. |
[35] | Cimdins A, Klinkert B, Aschke-Sonnenborn U, Kaiser F M, Kortmann J, Narberhaus F. Translational control of small heat shock genes in mesophilic and Thermophilic cyanobacteria by RNA thermometers [J]. RNA Biol., 2014, 11(5): 594-608. |
[36] | Deigan K E, Ferré-D'Amaré A R. Riboswitches: discovery of drugs that target bacterial gene-regulatory RNAs [J]. Accounts of Chemical Research, 2011, 44(12): 1329-1338. |
[37] | Li L. The biochemistry and physiology of metallic fluoride: action, mechanism, and implications [J]. Critical Reviews in Oral Biology & Medicine, 2003, 14(2): 100-114. |
[38] | Barbier O, Arreola-Mendoza L, Del Razo L M. Molecular mechanisms of fluoride toxicity [J]. Chem. Biol. Interact., 2010, 188(2): 319-333. |
[39] | Nelson J W, Zhou Z, Breaker R R. Gramicidin D enhances the antibacterial activity of fluoride [J]. Bioorg. Med. Chem. Lett., 2014, 24(13): 2969-2971. |
[40] | Fei X, Holmes T, Diddle J, Hintz L, Delaney D, Stock A, Renner D, McDevitt M, Berkowitz D B, Soukup J K. Phosphatase-inert glucosamine 6-phosphate mimics serve as actuators of the glmS riboswitch [J]. ACS Chem. Biol., 2014, 9(12): 2875-2882. |
[41] | Bren A, Eisenbach M. How signals are heard during bacterial chemo taxis: protein-protein interactions in sensory signal propagation [J]. J. Bacteriol., 2000, 182(24): 6865-6873. |
[42] | Topp S, Gallivan J P. Guiding bacteria with small molecules and RNA [J]. J. Am. Chem. Soc., 2007, 129(21): 6807-6811. |
[43] | Joshua K Michener, Christina D Smolke. High-throughput enzyme evolution in Saccharomyces cerevisiae using a synthetic RNA switch [J]. Metabolic Engineering, 2012, 14(4): 306-316. |
[44] | Zhu X, Wang X, Zhang C, Wang X, Gu Q. A riboswitch sensor to determine vitamin B12 in fermented foods [J]. Journal of Food Chem., 2015, 15(175): 523-528. |
[45] | Knudsen S M, Lee J, Ellington A D, Savran C A. Ribozyme-mediated signal augmentation on a aass-sensitive biosenser [J].J. Am. Chem. Soc., 2006, 128(50): 15936-15937. |
[46] | Paige J S, Wu K Y, Jaffrey S R. RNA mimics of green fluorescent protein [J]. Science, 2011, 333(6042): 642-646. |
[47] | Kellenberger C A, Wilson S C, Sales-Lee J, Hammond M C. RNA-based fluorescent biosensors for live cell imaging of second messengers cyclic di-GMP and cyclic AMP-GMP [J]. J. Am. Chem. Soc., 2013, 135(13): 4906-4909. |
[48] | Strack R L, Jaffrey S R. New approaches for sensing metabolites and proteins in live cells using RNA [J]. Curr. Opin. Chem. Biol., 2013, 17(4): 651-655. |
[49] | Nahvi A, Sudarsan N, Ebert M S, Zou X, Brown K L, Breaker R R. Genetic control by a metabolite binding mRNA [J]. Chem. Biol., 2002, 9(9): 1043-1049. |
[1] | Xin YANG, Wen WANG, Kai XU, Fanhua MA. Simulation analysis of temperature characteristics of the high-pressure hydrogen refueling process [J]. CIESC Journal, 2023, 74(S1): 280-286. |
[2] | Song HE, Qiaomai LIU, Guangshuo XIE, Simin WANG, Juan XIAO. Two-phase flow simulation and surrogate-assisted optimization of gas film drag reduction in high-concentration coal-water slurry pipeline [J]. CIESC Journal, 2023, 74(9): 3766-3774. |
[3] | Lei XING, Chunyu MIAO, Minghu JIANG, Lixin ZHAO, Xinya LI. Optimal design and performance analysis of downhole micro gas-liquid hydrocyclone [J]. CIESC Journal, 2023, 74(8): 3394-3406. |
[4] | Manzheng ZHANG, Meng XIAO, Peiwei YAN, Zheng MIAO, Jinliang XU, Xianbing JI. Working fluid screening and thermodynamic optimization of hazardous waste incineration coupled organic Rankine cycle system [J]. CIESC Journal, 2023, 74(8): 3502-3512. |
[5] | Chengying ZHU, Zhenlei WANG. Operation optimization of ethylene cracking furnace based on improved deep reinforcement learning algorithm [J]. CIESC Journal, 2023, 74(8): 3429-3437. |
[6] | Guoze CHEN, Dong WEI, Qian GUO, Zhiping XIANG. Optimal power point optimization method for aluminum-air batteries under load tracking condition [J]. CIESC Journal, 2023, 74(8): 3533-3542. |
[7] | Wenzhu LIU, Heming YUN, Baoxue WANG, Mingzhe HU, Chonglong ZHONG. Research on topology optimization of microchannel based on field synergy and entransy dissipation [J]. CIESC Journal, 2023, 74(8): 3329-3341. |
[8] | Wentao WU, Liangyong CHU, Lingjie ZHANG, Weimin TAN, Liming SHEN, Ningzhong BAO. High-efficient preparation of cardanol-based self-healing microcapsules [J]. CIESC Journal, 2023, 74(7): 3103-3115. |
[9] | Xiaoling TANG, Jiarui WANG, Xuanye ZHU, Renchao ZHENG. Biosynthesis of chiral epichlorohydrin by halohydrin dehalogenase based on Pickering emulsion system [J]. CIESC Journal, 2023, 74(7): 2926-2934. |
[10] | Chunlei ZHAO, Liang GUO, Cong GAO, Wei SONG, Jing WU, Jia LIU, Liming LIU, Xiulai CHEN. Metabolic engineering of Escherichia coli for chondroitin production [J]. CIESC Journal, 2023, 74(5): 2111-2122. |
[11] | Zedong WANG, Zhiping SHI, Liyan LIU. Numerical simulation and optimization of acoustic streaming considering inhomogeneous bubble cloud dissipation in rectangular reactor [J]. CIESC Journal, 2023, 74(5): 1965-1973. |
[12] | Xiaodan SU, Ganyu ZHU, Huiquan LI, Guangming ZHENG, Ziheng MENG, Fang LI, Yunrui YANG, Benjun XI, Yu CUI. Optimization of wet process phosphoric acid hemihydrate process and crystallization of gypsum [J]. CIESC Journal, 2023, 74(4): 1805-1817. |
[13] | Xiaoyong GAO, Fuyu HUANG, Wanpeng ZHENG, Diao PENG, Yixu YANG, Dexian HUANG. Scheduling optimization of refinery and chemical production process considering the safety and stability of scheduling operation [J]. CIESC Journal, 2023, 74(4): 1619-1629. |
[14] | Sheng’an ZHANG, Guilian LIU. Multi-objective optimization of high-efficiency solar water electrolysis hydrogen production system and its performance [J]. CIESC Journal, 2023, 74(3): 1260-1274. |
[15] | Xuerong GU, Shuoshi LIU, Siyu YANG. Research on multi-parameter optimization method based on parallel EGO and surrogate-assisted model [J]. CIESC Journal, 2023, 74(3): 1205-1215. |
Viewed | ||||||||||||||||||||||||||||||||||||||||||||||||||
Full text 1054
|
|
|||||||||||||||||||||||||||||||||||||||||||||||||
Abstract 475
|
|
|||||||||||||||||||||||||||||||||||||||||||||||||