Please wait a minute...

中国生物工程杂志

CHINA BIOTECHNOLOGY
中国生物工程杂志
中国生物工程杂志  2021, Vol. 41 Issue (1): 30-41    DOI: 10.13523/j.cb.2011007
综述     
羊毛硫肽的高通量工程改造方法新进展 *
郭二鹏,张建志(),司同()
中国科学院深圳先进技术研究院 深圳合成生物学创新研究院 深圳 518055
Recent Advances in the High-throughput Engineering of Lanthipeptides
GUO Er-peng,ZHANG Jian-zhi(),SI Tong()
Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen Institute of Synthetic Biology, Shenzhen 518055, China
 全文: PDF(43838 KB)   HTML
摘要：

羊毛硫肽(lanthipeptide)是由核糖体合成并经翻译后修饰产生的肽类天然产物,具有丰富的分子结构和多样的生物活性。新型羊毛硫肽是活性药物的重要来源,可以通过基因组挖掘和工程改造获得。羊毛硫肽前体肽由基因编码,同时其合成酶具有较高的底物杂泛性。基于这些特征,可以对羊毛硫肽的生物合成过程开展高通量工程改造,从而快速获得新的羊毛硫肽衍生物。综述了近些年高通量构建和筛选羊毛硫肽衍生物的新方法:介绍了非天然氨基酸引入、组合式生物合成、嵌合前导肽等文库构建技术;讨论了细胞表面展示、反向双杂交、细胞自裂解、无细胞(cell-free)体系等方法在结构与活性筛选中的应用;对基于自动化合成生物技术开展羊毛硫肽的规模化工程改造进行了展望。
关键词： 羊毛硫肽;  生物合成;  高通量筛选;  合成生物学;  细胞表面展示    
Abstract:

Lanthipeptides are a major class of ribosomally synthesized and posttranslationally modified peptides (RiPPs) with diverse molecular structures and biological activities. New lanthipeptides obtained by genome mining and engineering are an important source of drug leads. Lanthipeptides are particularly amenable to bioengineering because their precursor peptides are encoded by genes and biosynthetic enzymes often exhibit high promiscuity, which is helpful for the efficient construction of lanthipeptides derivatives. This paper reviews the recent advances in high-throughput creation and screening of lanthipeptide derivatives. For mutant library creation, we discuss the introduction of noncanonical amino acids (ncAAs), combinatorial biosynthesis, and chimeric-leader approach for creating hybrid RiPPs. Then, we introduce large-scale structural and activity screening of lanthipeptide mutants assisted by cell surface display, reverse two-hybrid system, cellular autolysis, cell-free system, and microfluidics. Finally, we present future perspectives on the use of synthetic biology automation to streamline lanthipeptide bioengineering.
Key words: Lanthipeptide    Biosynthesis    High-throughout screening    Synthetic biology    Cell surface-display
收稿日期: 2020-11-02 出版日期: 2021-02-09
ZTFLH:  Q819  
基金资助: * 国家重点研发计划(2020YFA0908501)
通讯作者: 张建志,司同     E-mail: zhangjz@siat.ac.cn;tong.si@siat.ac.cn
服务　　
把本文推荐给朋友
加入引用管理器
E-mail Alert
RSS
作者相关文章　　
郭二鹏
张建志
司同

引用本文:

郭二鹏, 张建志, 司同. 羊毛硫肽的高通量工程改造方法新进展 *[J]. 中国生物工程杂志, 2021, 41(1): 30-41.

GUO Er-peng, ZHANG Jian-zhi, SI Tong. Recent Advances in the High-throughput Engineering of Lanthipeptides. China Biotechnology, 2021, 41(1): 30-41.

链接本文:

https://manu60.magtech.com.cn/biotech/CN/10.13523/j.cb.2011007    或    https://manu60.magtech.com.cn/biotech/CN/Y2021/V41/I1/30

图1  羊毛硫肽生物合成机制
图2  羊毛硫肽衍生物文库的模块化构建与表征
图3  表面展示技术用于羊毛硫肽工程改造
[1] Arnison P G, Bibb M J, Bierbaum G, et al. Ribosomally synthesized and post-translationally modified peptide natural products: overview and recommendations for a universal nomenclature. Nature Product Reports, 2013,30:108-160.
[2] Repka L M, Chekan J R, Nair S K, et al. Mechanistic understanding of lanthipeptide biosynthetic enzymes. Chemical Reviews, 2017,117(8):5457-5520.
doi: 10.1021/acs.chemrev.6b00591 pmid: 28135077
[3] McIntosh J A, Donia M S, Schmidt E W. Ribosomal peptide natural products: bridging the ribosomal and nonribosomal worlds. Cheminform, 2009,26(4):537-559.
[4] Funk M A, Van der Donk W A. Ribosomal natural products, tailored to fit. Accounts of Chemical Research, 2017,50(7):1577-1586.
[5] Shin J M, Gwak J W, Kamarajan P, et al. Biomedical applications of nisin. Journal of Applied Microbiology, 2016,120(6):1449-1465.
pmid: 26678028
[6] Cotter P D, Ross R P, Hill C. Bacteriocins - a viable alternative to antibiotics. Nature Reviews Microbiology, 2013,11(2):95-105.
doi: 10.1038/nrmicro2937 pmid: 23268227
[7] Hillman J D. Genetically modified Streptococcus mutans for the prevention of dental caries. Antonie van Leeuwenhoek, 2002,82:361-366.
pmid: 12369203
[8] Märki F, Hänni E, Fredenhagen A, et al. Mode of action of the lanthionine-containing peptide antibiotics duramycin, duramycin B and C, and cinnamycin as indirect inhibitors of phospholipase A2. Biochemical Pharmacology, 1991,42(10):2027-2035.
pmid: 1741778
[9] Krawczyk J M, Voller G H, Krawczyk B, et al. Heterologous expression and engineering studies of labyrinthopeptins, class III lantibiotics from actinomadura namibiensis. Chemistry & Biology, 2013,20(1):111-122.
doi: 10.1016/j.chembiol.2012.10.023 pmid: 23352145
[10] Ferir G, Petrova M I, Andrei G, et al. The lantibiotic peptide labyrinthopeptin a1 demonstrates broad anti-hiv and anti-hsv activity with potential for microbicidal applications. PLoS One, 2013,8(5):e64010.
pmid: 23724015
[11] Meindl K, Schmiederer T, Schneider K, et al. Labyrinthopeptins: a new class of carbacyclic lantibiotics. Angewandte Chemie International Edition, 2010,49(6):1151-1154.
doi: 10.1002/anie.200905773 pmid: 20082397
[12] Prestinaci F, Pezzotti P, Pantosti A. Antimicrobial resistance: a global multifaceted phenomenon. Pathogens & Global Health, 2015,109(7):309-318.
pmid: 26343252
[13] Li B, Sher D, Kelly L, et al. Catalytic promiscuity in the biosynthesis of cyclic peptide secondary metabolites in planktonic marine cyanobacteria. Proceedings of the National Academy of Sciences, 2010,107(23):10430-10435.
[14] Van Hell A J, Kloosterman T G, Montalban-Lopez M. Discovery, production and modification of five novel lantibiotics using the promiscuous nisin modification machinery. ACS Synthetic Biology, 2016,5(10):1146-1154.
doi: 10.1021/acssynbio.6b00033 pmid: 27294279
[15] Van Staden A D P, Faure L M, Vermeulen R R, et al. Functional expression of gfp-fused class I lanthipeptides in Escherichia coli. ACS Synthetic Biology, 2019,8(10):2220-2227.
pmid: 31553571
[16] Field D, Cotter P D, Hill C, et al. Bioengineering lantibiotics for therapeutic success. Frontiers in Microbiology, 2015,6:1363.
doi: 10.3389/fmicb.2015.01363 pmid: 26640466
[17] Montalban-Lopez M, Van Heel A J, Kuipers O P. Employing the promiscuity of lantibiotic biosynthetic machineries to produce novel antimicrobials. Fems Microbiology Reviews, 2017,41(1):5-18.
pmid: 27591436
[18] Field D, Begley M, O’Connor P M, et al. Bioengineered nisin a derivatives with enhanced activity against both gram positive and gram negative pathogens. PLoS One, 2012,7(10):e46884.
doi: 10.1371/journal.pone.0046884 pmid: 23056510
[19] Breukink E, de Kruijff B. Lipid II as a target for antibiotics. Nature Reviews Drug Discovery, 2006,5(4):321-332.
pmid: 16531990
[20] Zhou L, Van Heel A J, Kuipers O P. The length of a lantibiotic hinge region has profound influence on antimicrobial activity and host specificity. Frontiers in Microbiology, 2015,6:11.
doi: 10.3389/fmicb.2015.00011 pmid: 25688235
[21] Si T, Tian Q, Min Y, et al. Rapid screening of lanthipeptide analogs via in-colony removal of leader peptides in Escherichia coli. Journal of the American Chemical Society, 2018,140(38):11884-11888.
doi: 10.1021/jacs.8b05544 pmid: 30183279
[22] Barbosa J, Caetano T, Mosker E, et al. Lichenicidin rational site-directed mutagenesis library: a tool to generate bioengineered lantibiotics. Biotechnology and Bioengineering, 2019,116(11):3053-3062.
doi: 10.1002/bit.27130 pmid: 31350903
[23] Field D, Molloy E M, Iancu C, et al. Saturation mutagenesis of selected residues of the α-peptide of the lantibiotic lacticin 3 147 yields a derivative with enhanced antimicrobial activity. Microbial Biotechnology, 2013,6(5):564-575.
pmid: 23433070
[24] Kers J A, Sharp R E, Muley S, et al. Blueprints for the rational design of therapeutic mutacin 1 140 variants. Chemical Biology & Drug Design, 2018,92(6):1940-1953.
doi: 10.1111/cbdd.13365 pmid: 30010233
[25] Escano J, Ravichandran A, Salamat B, et al. Carboxyl analogue of mutacin 1 140, a scaffold for lead antibacterial discovery. Applied and Environmental Microbiology, 2017,83(14):e00668-17.
doi: 10.1128/AEM.00668-17 pmid: 28500042
[26] Kers J A, Sharp R E, Defusco A W, et al. Mutacin 1 140 lantibiotic variants are efficacious against clostridium difficile infection. Frontiers in Microbiology, 2018,9:415.
pmid: 29615987
[27] Schmitt S, Montalban-Lopez M, Peterhoff D, et al. Analysis of modular bioengineered antimicrobial lanthipeptides at nanoliter scale. Nature Chemical Biology, 2019,15(5):437-443.
doi: 10.1038/s41589-019-0250-5 pmid: 30936500
[28] Baumann T, Nickling J H, Bartholomae M, et al. Prospects of in vivo incorporation of non-canonical amino acids for the chemical diversification of antimicrobial peptides. Frontiers in Microbiology, 2017,8:124.
[29] Budisa N. Expanded genetic code for the engineering of ribosomally synthetized and post-translationally modified peptide natural products (RiPPs). Current Opinion in Biotechnology, 2013,24(4):591-598.
pmid: 23537814
[30] Buer B C, Marsh E N. Fluorine: A new element in protein design. Protein Science, 2012,21(4):453-462.
[31] An L, Van der Donk W A. Recent progress in lanthipeptide biosynthesis, discovery, and engineering. Compre hersive products III. 3 rd ed . Elsevier, 2020: 119-165.
[32] Levengood M R, Knerr P J, Oman T J, et al. In vitro mutasynthesis of lantibiotic analogues containing nonproteinogenic amino acids. Journal of the American Chemical Society, 2009,131(34):12024-12025.
doi: 10.1021/ja903239s pmid: 19655738
[33] Johnson J A, Lu Y Y, Van Deventer J A, et al. Residue-specific incorporation of non-canonical amino acids into proteins: recent developments and applications. Current Opinion in Chemical Biology, 2010,14(6):774-780.
[34] Zhou L, Shao J, Li Q, et al. Incorporation of tryptophan analogues into the lantibiotic nisin. Amino Acids, 2016,48:1309-1318.
doi: 10.1007/s00726-016-2186-3 pmid: 26872656
[35] Stromgaard A, Jensen A A, Stromgaard K. Site-specific incorporation of unnatural amino acids into proteins. Chembiochen, 2004,5(7):909-916.
[36] Shi Y X, Yang X, Garg N, et al. Production of lantipeptides in Escherichia coli. Journal of the American Chemical Society, 2011,133(8):2338-2341.
pmid: 21114289
[37] Bindman N A, Bobeica S C, Liu W R, et al. Facile removal of leader peptides from lanthipeptides by incorporation of a hydroxy acid. Journal of the American Chemical Society, 2015,137(22):6975-6978.
pmid: 26006047
[38] Kakkar N, Perez J G, Liu W R, et al. Incorporation of nonproteinogenic amino acids in class i and ii lantibiotics. ACS Chemical Biology, 2018,13(4):951-957.
pmid: 29439566
[39] Gan Q L, Fan C G. Increasing the fidelity of noncanonical amino acid incorporation in cell-free protein synthesis. Biochimica et Biophysica Acta (BBA)-General Subjects, 2017,1861(11Pt B):3047-3052.
[40] Pokrovskaya V, Belakhov V, Hainrichson M, et al. Design, synthesis, and evaluation of novel fluoroquinolone-aminoglycoside hybrid antibiotics. Journal of Medicinal Chemistry, 2009,52(8):2243-2254.
doi: 10.1021/jm900028n pmid: 19301822
[41] Wiedemann I, Breukink E, Van Kraaij C, et al. Specific binding of nisin to the peptidoglycan precursor lipid ii combines pore formation and inhibition of cell wall biosynthesis for potent antibiotic activity. The Journal of Biological Chemistry, 2001,276(3):1772-1779.
pmid: 11038353
[42] Mccomas C C, Crowley B M, Boger D L . Partitioning the loss in vancomycin binding affinity for D-Ala-D-Lac into lost H-bond and repulsive lone pair contributions. Journal of the American Chemical Society, 2003,125(31):9314-9315.
doi: 10.1021/ja035901x pmid: 12889959
[43] Arnusch C J, Bonvin A M J J, Verel A M, et al. The vancomycin-nisin(1-12) hybrid restores activity against vancomycin resistant Enterococci. Biochemistry, 2008,47(48):12661-12663.
doi: 10.1021/bi801597b pmid: 18989934
[44] Helander I M, Mattila-Sandholm T . Permeability barrier of the gram-negative bacterial outer membrane with special reference to nisin. International Journal of Food Microbiology, 2000,60(2-3):153-161.
pmid: 11016605
[45] Bechinger B, Gorr S U. Antimicrobial peptides: mechanisms of action and resistance. Journal of Dental Research, 2017,96(3):254-260.
pmid: 27872334
[46] Li Q, Montalban-Lopez M, Kuipers O P. Increasing the antimicrobial activity of nisin-based lantibiotics against gram-negative pathogens. Applied and Environmental Microbiology, 2018,84(12):e00052-18.
doi: 10.1128/AEM.00052-18 pmid: 29625984
[47] Codd R, Richardson-Sanchez T, Telfer T J, et al. Advances in the chemical biology of desferrioxamine b. ACS Chemical Biology, 2018,13(1):11-25.
pmid: 29182270
[48] Yoganathan S, Sit C S, Vederas J C. Chemical synthesis and biological evaluation of gallidermin-siderophore conjugates. Organic & Biomolecular Chemistry, 2011,9(7):2133-2141.
pmid: 21290068
[49] Götz F, Perconti S, Popella P, et al. Epidermin and gallidermin: Staphylococcal lantibiotics. International Journal of Medical Microbiology, 2014,304(1):63-71.
doi: 10.1016/j.ijmm.2013.08.012
[50] Van Heel A J, Mu D, Montalbán-López M, et al. Designing and producing modified, new-to-nature peptides with antimicrobial activity by use of a combination of various lantibiotic modification enzymes. ACS Synthetic Biology, 2013,2(7):397-404.
doi: 10.1021/sb3001084 pmid: 23654279
[51] Burkhart B J, Kakkar N, Hudson G A, et al. Chimeric leader peptides for the generation of non-natural hybrid PiPP products. ACS Central Science, 2017,3(6):629-638.
doi: 10.1021/acscentsci.7b00141
[52] Löfblm J. Bacterial display in combinatorial protein engineering. Biotechnology Journal, 2011,6(9):1115-1129.
doi: 10.1002/biot.201100129 pmid: 21786423
[53] Bosma T, Kuipers A, Bulten E, et al. Bacterial display and screening of posttranslationally thioether-stabilized peptides. Applied and Environmental Microbiology, 2011,77(19):6794-6801.
doi: 10.1128/AEM.05550-11
[54] Kieke M C, Cho B K, Boder E T, et al. Isolation of anti-T cell receptor scFv mutants by yeast surface display. Protein Engineering, 1997,10(11):1303-1310.
doi: 10.1093/protein/10.11.1303 pmid: 9514119
[55] Andreu C, Del Olmo M L. Yeast arming systems: pros and cons of different protein anchors and other elements required for display. Applied Microbiology and Biotechnology, 2018,102(6):2543-2561.
doi: 10.1007/s00253-018-8827-6 pmid: 29435617
[56] McMahon C, Baier A S, Pascolutti R, et al. Yeast surface display platform for rapid discovery of conformationally selective nanobodies. Nature Structural & Molecular Biology, 2018,25(3):289-296.
doi: 10.1038/s41594-018-0028-6 pmid: 29434346
[57] Hetrick K J, Walker M C, Van der Donk W A. Development and application of yeast and phage display of diverse lanthipeptides. ACS Central Science, 2018,4(4):458-467.
doi: 10.1021/acscentsci.7b00581 pmid: 29721528
[58] Urban J H, Moosmeier M A, Aumuller T, et al. Phage display and selection of lanthipeptides on the carboxy-terminus of the gene-3 minor coat protein. Nature Communications, 2017,8(1):1500.
doi: 10.1038/s41467-017-01413-7 pmid: 29138389
[59] Huang Y, Wiedmann M M, Suga H. RNA display methods for the discovery of bioactive macrocycles. Chemical Reviews, 2019,119(17):10360-10391.
doi: 10.1021/acs.chemrev.8b00430 pmid: 30395448
[60] Hofmann F T, Szostak J W, Seebeck F P. In vitro selection of functional lantipeptides. Journal of the American Chemical Society, 2012,134(19):8038-8041.
doi: 10.1021/ja302082d
[61] Yang X, Lennard K R, He C, et al. A lanthipeptide library used to identify a protein-protein interaction inhibitor. Nature Chemical Biology, 2018,14(4):375-380.
doi: 10.1038/s41589-018-0008-5 pmid: 29507389
[62] Cheng F, Takala T M, Saris P E. Nisin biosynthesis in vitro. Journal of Molecular Microbiology and Biotechnology, 2007,13(4):248-254.
doi: 10.1159/000104754 pmid: 17827976
[63] Liu R, Zhang Y C, Zhai G Q, et al. A cell-free platform based on nisin biosynthesis for discovering novel lanthipeptides and guiding their overproduction in vivo. Advanced Science, 2020,7(17):2001616.
doi: 10.1002/advs.202001616 pmid: 32995136
[64] Hillson N, Caddick M, Cai Y, et al. Building a global alliance of biofoundries. Nature Communications, 2019,10:2040.
doi: 10.1038/s41467-019-10079-2 pmid: 31068573
[65] 张建志, 付立豪, 唐婷, 等. 基于合成生物学策略的酶蛋白元件规模化挖掘. 合成生物学, 2020,1(3):319-336.
Zhang J Z, Fu L H, Tang T, et al. Scalable mining of proteins for biocatalysis via synthetic biology. Synthetic Biology Journal, 2020,1(3):319-336.
[66] 唐婷, 付立豪, 郭二鹏, 等. 自动化合成生物技术与工程化设施平台. 科学通报. [2021-01-23]. http://kns.cnki.net/kcms/detail/11.1784.N.20210122.1405.002.html.
Tang T, Fu L H, Guo E P, et al. Automation in synthetic biology using biological foundries. Chinese Science Bulletin.[2021-01-23]. http://kns.cnki.net/kcms/detail/11.1784.N.20210122.1405.002.html.
[1] 马宁,王汉杰. 光遗传学在细菌生产调控中的应用进展[J]. 中国生物工程杂志, 2021, 41(9): 101-109.
[2] 黄焕邦,吴洋,杨友辉,王兆官,齐浩. 基于古菌酪氨酰tRNA合成酶非天然氨基酸插入的研究进展[J]. 中国生物工程杂志, 2021, 41(9): 110-125.
[3] 郭芳,张良,冯旭东,李春. 植物源UDP-糖基转移酶及其分子改造*[J]. 中国生物工程杂志, 2021, 41(9): 78-91.
[4] 张恒,刘慧燕,潘琳,王红燕,李晓芳,王彤,方海田. 生物法合成γ-氨基丁酸的研究策略*[J]. 中国生物工程杂志, 2021, 41(8): 110-119.
[5] 郭曼曼,田开仁,乔建军,李艳妮. 噬菌体重组酶系统在合成生物学中的应用*[J]. 中国生物工程杂志, 2021, 41(8): 90-102.
[6] 李冰,张传波,宋凯,卢文玉. 生物合成稀有人参皂苷的研究进展*[J]. 中国生物工程杂志, 2021, 41(6): 71-88.
[7] 苗轶男,李敬知,王帅,李春,王颖. 萜烯生物合成中关键酶的研究进展*[J]. 中国生物工程杂志, 2021, 41(6): 60-70.
[8] 翟君叶,成旭,孙泽敏,李春,吕波. 毛蕊花糖苷的生物合成研究进展[J]. 中国生物工程杂志, 2021, 41(5): 94-104.
[9] 董曙馨,秦磊,李春,李珺. 利用转录因子工程重塑代谢网络实现细胞工厂高效生产[J]. 中国生物工程杂志, 2021, 41(4): 55-63.
[10] 栗波,王泽建,梁剑光,刘爱军,李海东. 等离子体作用结合氧限制模型选育利福霉素SV高产菌株 *[J]. 中国生物工程杂志, 2021, 41(2/3): 38-44.
[11] 范雁,杨淼,薛松. 基于光谱法-图像灰度法高通量筛选高效固定CO2的苯甲酸脱羧酶*[J]. 中国生物工程杂志, 2021, 41(11): 55-63.
[12] 郑义,郭世英,隋凤翔,杨骐羽,卫雅萱,李晓岩. 群体感应系统在合成生物学中的应用*[J]. 中国生物工程杂志, 2021, 41(11): 100-109.
[13] 王光路, 王梦园, 周忆菲, 马科, 张帆, 杨雪鹏. 吡咯喹啉醌生物合成研究进展 *[J]. 中国生物工程杂志, 2021, 41(1): 103-113.
[14] 察亚平, 朱牧孜, 李爽. 体内连续定向进化研究进展 *[J]. 中国生物工程杂志, 2021, 41(1): 42-51.
[15] 常璐, 黄娇芳, 董浩, 周斌辉, 朱小娟, 庄英萍. 合成生物学改造微生物及生物被膜用于重金属污染检测与修复 *[J]. 中国生物工程杂志, 2021, 41(1): 62-71.
主管：中国科学院 　主办：中国科学院文献情报中心 　中国生物技术发展中心 　中国生物工程学会