2025年4月17日 周四
首页 > 过刊浏览>2017年第57卷第11期 >1735-1746. DOI:10.13343/j.cnki.wsxb.20170332
PDF HTML阅读 XML下载 导出引用 引用提醒
Red/ET同源重组技术及其在微生物基因组挖掘中的应用进展
作者:
基金项目:

国家自然科学基金（31500033，31670097，31670098）；国家重点研发计划（2017YFD0201405）


Advances in Red/ET recombineering and its application for microbial genome mining
Author:
  • 摘要
    • | |
  • 访问统计
    • |
  • 参考文献 [57]
    • |
  • 相似文献 [20]
    • | | |
  • 文章评论
    摘要:

    Red/ET同源重组技术（Red/ET recombineering）是由来源于大肠杆菌λ噬菌体的蛋白对Redα/Redβ或来源于Rac原噬菌体的蛋白对RecE/RecT所介导的基于短同源臂（40-50 bp）的同源重组技术，能对宿主DNA序列进行快速、高效、精确的修饰和操作。本文主要综述了2010年以来Red/ET同源重组技术在大肠杆菌及其他细菌中的研究进展，同时简要介绍了该技术在微生物基因组挖掘，尤其是在微生物基因簇的异源表达领域的应用进展。

    Abstract:

    Red/ET recombineering is an in vivo homologous recombination-based genetic engineering method used primarily in Escherichia coli by using short homology arms (40-50 bp), based on the expression of either redα/redβ from the Red operon of λ phage or the analogous recE/recT from Rac prophage that are located in the E. coli chromosome. It can rapidly, efficiently and accurately modify and manipulate genomic and episome DNA. In this review, we introduce the progress of Red/ET recombineering in E. coli and other bacteria, and its application in microbial genome mining, especially in the field of heterologous expression of microbial biosynthetic gene clusters.

    参考文献
    [1] Zhang YM, Buchholz F, Muyrers JPP, Stewart AF. A new logic for DNA engineering using recombination in Escherichia coli. Nature Genetics, 1998, 20(2):123-128.
    [2] Muyrers JPP, Zhang YM, Testa G, Stewart AF. Rapid modification of bacterial artificial chromosomes by ET-recombination. Nucleic Acids Research, 1999, 27(6):1555-1557.
    [3] Zhang YM, Muyrers JPP, Rientjes J, Stewart AF. Phage annealing proteins promote oligonucleotide-directed mutagenesis in Escherichia coli and mouse ES cells. BMC Molecular Biology, 2003, 4(1):1.
    [4] Muyrers JPP, Zhang YM, Stewart AF. Techniques:recombinogenic engineering-new options for cloning and manipulating DNA. Trends in Biochemical Sciences, 2001, 26(5):325-331.
    [5] Sharan SK, Thomason LC, Kuznetsov SG, Court DL. Recombineering:a homologous recombination-based method of genetic engineering. Nature Protocols, 2009, 4(2):206-223.
    [6] Little JW. An exonuclease induced by bacteriophage λ Ⅱ. Nature of the enzymatic reaction. Journal of Biological Chemistry, 1967, 242(4):679-686.
    [7] Karakousis G, Ye N, Li Z, Chiu SK, Reddy G, Radding CM. The beta protein of phage λ binds preferentially to an intermediate in DNA renaturation. Journal of Molecular Biology, 1998, 276(4):721-731.
    [8] Li Z, Karakousis G, Chiu SK, Reddy G, Radding CM. The beta protein of phage λ promotes strand exchange. Journal of Molecular Biology, 1998, 276(4):733-744.
    [9] Fu J, Bian XY, Hu S, Wang HL, Huang F, Seibert PM, Plaza A, Xia LQ, Müller R, Stewart AF, Zhang YM. Full-length RecE enhances linear-linear homologous recombination and facilitates direct cloning for bioprospecting. Nature Biotechnology, 2012, 30(5):440-446.
    [10] Cobb RE, Zhao HM. Direct cloning of large genomic sequences. Nature Biotechnology, 2012, 30(5):405-406.
    [11] Nawy T. Molecular biology:capturing sequences for bioprospecting. Nature Methods, 2012, 9(6):532.
    [12] Wang HH, Isaacs FJ, Carr PA, Sun ZZ, Xu G, Forest CR, Church GM. Programming cells by multiplex genome engineering and accelerated evolution. Nature, 2009, 460(7257):894-898.
    [13] Isaacs FJ, Carr PA, Wang HH, Lajoie MJ, Sterling B, Kraal L, Tolonen AC, Gianoulis TA, Goodman DB, Reppas NB, Emig CJ, Bang D, Hwang SJ, Jewett MC, Jacobson JM, Church GM. Precise manipulation of chromosomes in vivo enables genome-wide codon replacement. Science, 2011, 333(6040):348-353.
    [14] Wang HH, Kim H, Cong L, Jeong J, Bang D, Church GM. Genome-scale promoter engineering by coselection MAGE. Nature Methods, 2012, 9(6):591-593.
    [15] Bird AW, Erler A, Fu J, Hériché JK, Maresca M, Zhang YM, Hyman AA, Stewart AF. High-efficiency counterselection recombineering for site-directed mutagenesis in bacterial artificial chromosomes. Nature Methods, 2011, 9(1):103-109.
    [16] Wang HL, Bian XY, Xia LQ, Ding XZ, Müller R, Zhang YM, Fu J, Stewart AF. Improved seamless mutagenesis by recombineering using ccdB for counterselection. Nucleic Acids Research, 2014, 42(5):e37.
    [17] Mosberg JA, Gregg CJ, Lajoie MJ, Wang HH, Church GM. Improving lambda red genome engineering in Escherichia coli via rational removal of endogenous nucleases. PLoS One, 2012, 7(9):e44638.
    [18] Thomason LC, Costantino N, Court DL. Examining a DNA replication requirement for bacteriophage λ red-and rac prophage RecET-promoted recombination in Escherichia coli. mBio, 2016, 7(5):e01443-16.
    [19] Subramaniam S, Erler A, Fu J, Kranz A, Tang J, Gopalswamy M, Ramakrishnan S, Keller A, Grundmeier G, Müller D, Sattler M, Stewart AF. DNA annealing by Redβ is insufficient for homologous recombination and the additional requirements involve intra-and inter-molecular interactions. Scientific Reports, 2016, 6:34525.
    [20] Hu K, Shi ZX, Wang HL, Feng EL, Huang LY. Study on gene knockout using Red system in Shigella flexneri. Acta Microbiologica Sinica, 2003, 43(6):740-746. (in Chinese)胡堃, 史兆兴, 王恒樑, 冯尔玲, 黄留玉. Red重组系统在痢疾杆菌基因敲除中的应用研究. 微生物学报, 2003, 43(6):740-746.
    [21] Karlinsey JE, Hughes KT. Genetic transplantation:Salmonella enterica serovar Typhimurium as a host to study sigma factor and anti-sigma factor interactions in genetically intractable systems. Journal of Bacteriology, 2006, 188(1):103-114.
    [22] Hu SB, Fu J, Huang F, Ding XZ, Stewart AF, Xia LQ, Zhang YM. Genome engineering of Agrobacterium tumefaciens using the lambda Red recombination system. Applied Microbiology and Biotechnology, 2014, 98(5):2165-2172.
    [23] Kang Y, Norris MH, Wilcox BA, Tuanyok A, Keim PS, Hoang TT. Knockout and pullout recombineering for naturally transformable Burkholderia thailandensis and Burkholderia pseudomallei. Nature Protocols, 2011, 6(8):1085-1104.
    [24] van Kessel JC, Hatfull GF. Recombineering in Mycobacterium tuberculosis. Nature Methods, 2007, 4(2):147-152.
    [25] van Kessel JC, Hatfull GF. Efficient point mutagenesis in mycobacteria using single-stranded DNA recombineering:characterization of antimycobacterial drug targets. Molecular Microbiology, 2008, 67(5):1094-1107.
    [26] van Pijkeren JP, Neoh KM, Sirias D, Findley AS, Britton RA. Exploring optimization parameters to increase ssDNA recombineering in Lactococcus lactis and Lactobacillus reuteri. Bioengineered, 2012, 3(4):209-217.
    [27] Swingle B, Bao ZM, Markel E, Chambers A, Cartinhour S. Recombineering using RecTE from Pseudomonas syringae. Applied and Environmental Microbiology, 2010, 76(15):4960-4968.
    [28] Yin J, Zhu HB, Xia LQ, Ding XZ, Hoffmann T, Hoffmann M, Bian XY, Müller R, Fu J, Stewart AF, Zhang YM. A new recombineering system for Photorhabdus and Xenorhabdus. Nucleic Acids Research, 2015, 43(6):e36.
    [29] Bode HB Jr, Müller R. The impact of bacterial genomics on natural product research. Angewandte Chemie International Edition, 2005, 44(42):6828-6846.
    [30] Cimermancic P, Medema MH, Claesen J, Kurita K, Wieland Brown LC, Mavrommatis K, Pati A, Godfrey PA, Koehrsen M, Clardy J, Birren BW, Takano E, Sali J, Linington RG, Fischbach MA. Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters. Cell, 2014, 158(2):412-421.
    [31] Zarins-Tutt JS, Barberi TT, Gao H, Mearns-Spragg A, Zhang LX, Newman DJ, Goss RJM. Prospecting for new bacterial metabolites:a glossary of approaches for inducing, activating and upregulating the biosynthesis of bacterial cryptic or silent natural products. Natural Product Reports, 2016, 33(1):54-72.
    [32] Rutledge PJ, Challis GL. Discovery of microbial natural products by activation of silent biosynthetic gene clusters. Nature Reviews Microbiology, 2015, 13(8):509-523.
    [33] Nett M. Genome mining:concept and strategies for natural product discovery//Kinghorn AD, Falk H, Kobayashi J. Progress in the Chemistry of Organic Natural Products. Cham:Springer, 2014:199-245.
    [34] Bachmann BO, Van Lanen SG, Baltz RH. Microbial genome mining for accelerated natural products discovery:is a renaissance in the making? Journal of Industrial Microbiology & Biotechnology, 2014, 41(2):175-184.
    [35] Yin J, Wang HL, Li RJ, Ravichandran V, Bian XY, Li AY, Tu Q, Stewart AF, Fu J, Zhang YM. A practical guide to recombineering in Photorhabdus and Xenorhabdus//ffrenchConstant RH. The Molecular Biology of Photorhabdus Bacteria. Cham:Springer, 2017:195-213.
    [36] Ongley SE, Bian XY, Neilan BA, Müller R. Recent advances in the heterologous expression of microbial natural product biosynthetic pathways. Natural Product Reports, 2013, 30(8):1121-1138.
    [37] Wenzel SC, Gross F, Zhang YM, Fu J, Stewart AF, Müller R. Heterologous expression of a myxobacterial natural products assembly line in pseudomonads via Red/ET recombineering. Chemistry & Biology, 2005, 12(3):349-356.
    [38] Perlova O, Fu J, Kuhlmann S, Krug D, Stewart AF, Zhang YM, Müller R. Reconstitution of the myxothiazol biosynthetic gene cluster by Red/ET recombination and heterologous expression in Myxococcus xanthus. Applied and Environmental Microbiology, 2006, 72(12):7485-7494.
    [39] Binz TM, Wenzel SC, Schnell HJ, Bechthold A, Müller R. Heterologous expression and genetic engineering of the phenalinolactone biosynthetic gene cluster by using Red/ET recombineering. ChemBioChem, 2008, 9(3):447-454.
    [40] Hu YF, Phelan VV, Farnet CM, Zazopoulos E, Bachmann BO. Reassembly of anthramycin biosynthetic gene cluster by using recombinogenic cassettes. ChemBioChem, 2008, 9(10):1603-1608.
    [41] Wolpert M, Heide L, Kammerer B, Gust B. Assembly and heterologous expression of the coumermycin A1 gene cluster and production of new derivatives by genetic engineering. ChemBioChem, 2008, 9(4):603-612.
    [42] Fu J, Wenzel SC, Perlova O, Wang JP, Gross F, Tang ZR, Yin YL, Stewart AF, Müller R, Zhang YM. Efficient transfer of two large secondary metabolite pathway gene clusters into heterologous hosts by transposition. Nucleic Acids Research, 2008, 36(17):e113.
    [43] Bian XY, Tang B, Yu YC, Tu Q, Gross F, Wang HL, Li AY, Fu JM, Shen Y, Li YZ, Stewart AF, Zhao GP, Ding XM, Müller R, Zhang YM. Heterologous production and yield improvement of epothilones in Burkholderiales strain DSM7029. ACS Chemical Biology, 2017, 12(7):1805-1812.
    [44] Chai Y, Shan SP, Weissman KJ, Hu SB, Zhang YM, Müller R. Heterologous expression and genetic engineering of the tubulysin biosynthetic gene cluster using Red/ET recombineering and inactivation mutagenesis. Chemistry & Biology, 2012, 19(3):361-371.
    [45] Kolinko I, Lohße A, Borg S, Raschdorf O, Jogler C, Tu Q, Pósfai M, Tompa É, Plitzko JM, Brachmann A, Wanner G, Müller, Zhang YM, Schüler D. Biosynthesis of magnetic nanostructures in a foreign organism by transfer of bacterial magnetosome gene clusters. Nature Nanotechnology, 2014, 9(3):193-197.
    [46] Bian XY, Huang F, Wang HL, Klefisch T, Müller R, Zhang YM. Heterologous production of glidobactins/luminmycins in Escherichia coli Nissle containing the glidobactin biosynthetic gene cluster from Burkholderia DSM7029. ChemBioChem, 2014, 15(15):2221-2224.
    [47] Ongley SE, Bian XY, Zhang YM, Chau R, Gerwick WH, Müller R, Neilan BA. High-titer heterologous production in E. coli of lyngbyatoxin, a protein kinase C activator from an uncultured marine cyanobacterium. ACS Chemical Biology, 2013, 8(9):1888-1893.
    [48] Kodumal SJ, Patel KG, Reid R, Menzella HG, Welch M, Santi DV. Total synthesis of long DNA sequences:synthesis of a contiguous 32-kb polyketide synthase gene cluster. Proceedings of the National Academy of Sciences of the United States of America, 2004, 101(44):15573-15578.
    [49] Tu Q, Herrmann J, Hu SB, Raju R, Bian XY, Zhang Y,M Müller R. Genetic engineering and heterologous expression of the disorazol biosynthetic gene cluster via Red/ET recombineering. Scientific Reports, 2016, 6:21066.
    [50] Bian XY, Huang F, Stewart AF, Xia LQ, Zhang YM, Müller R. Direct cloning, genetic engineering, and heterologous expression of the syringolin biosynthetic gene cluster in E. coli through Red/ET recombineering. ChemBioChem, 2012, 13(13):1946-1952.
    [51] Bian XY, Plaza A, Zhang YM, Müller R. Luminmycins A-C, cryptic natural products from photorhabdus luminescens identified by heterologous expression in Escherichia coli. Journal of Natural Products, 2012, 75(9):1652-1655.
    [52] Liu QS, Shen QY, Bian XY, Chen HN, Fu J, Wang HL, Lei P, Guo ZH, Chen W, Li DJ, Zhang YM. Simple and rapid direct cloning and heterologous expression of natural product biosynthetic gene cluster in Bacillus subtilis via Red/ET recombineering. Scientific Reports, 2016, 6:34623.
    [53] Yin J, Hoffmann M, Bian XY, Tu Q, Yan F, Xia LQ, Ding XZ, Stewart AF, Müller R, Fu J, Zhang YM. Direct cloning and heterologous expression of the salinomycin biosynthetic gene cluster from Streptomyces albus DSM41398 in Streptomyces coelicolor A3(2). Scientific Reports, 2015, 5:15081.
    [54] Wang HL, Li Z, Jia RN, Hou Y, Yin J, Bian XY, Li AY, Müller R, Stewart AF, Fu J, Zhang YM. RecET direct cloning and Red αβ recombineering of biosynthetic gene clusters, large operons or single genes for heterologous expression. Nature Protocols, 2016, 11(7):1175-1190.
    [55] Bian XY, Fu J, Plaza A, Herrmann J, Pistorius D, Stewart AF, Zhang YM, Müller R. In vivo evidence for a prodrug activation mechanism during colibactin maturation. ChemBioChem, 2013, 14(10):1194-1197.
    [56] Bian XY, Plaza A, Yan F, Zhang YM, Müller R. Rational and efficient site-directed mutagenesis of adenylation domain alters relative yields of luminmide derivatives in vivo. Biotechnology and Bioengineering, 2015, 112(7):1343-1353.
    [57] Perlova O, Gerth K, Kuhlmann S, Zhang YM, Müller R. Novel expression hosts for complex secondary metabolite megasynthetases:production of myxochromide in the thermopilic isolate Corallococcus macrosporus GT-2. Microbial Cell Factories, 2009, 8:1.
    引证文献
    网友评论
    网友评论
    分享到微博
    发 布
引用本文

郑文韬,张友明,卞小莹. Red/ET同源重组技术及其在微生物基因组挖掘中的应用进展[J]. 微生物学报, 2017, 57(11): 1735-1746

复制
分享
文章指标
  • 点击次数:1406
  • 下载次数: 5932
  • HTML阅读次数: 1410
  • 引用次数: 0
历史
  • 收稿日期:2017-07-04
  • 最后修改日期:2017-08-12
  • 在线发布日期: 2017-10-30
文章二维码

科微学术

微生物学报

您是本站第 5676982 访问者

通信地址：北京市朝阳区北辰西路1号院3号 中国科学院微生物研究所   邮编：100101

电话：010-64807516    E-mail：actamicro@im.ac.cn

版权所有：微生物学报 ® 2025 版权所有