基于古菌酪氨酰tRNA合成酶非天然氨基酸插入的研究进展

doi:10.13523/j.cb.2104047

中国生物工程杂志

2021, Vol. 41

Issue (9): 110-125 DOI: 10.13523/j.cb.2104047

综述

基于古菌酪氨酰tRNA合成酶非天然氨基酸插入的研究进展

黄焕邦^1,^2,³,吴洋^1,^2,³,杨友辉^1,^2,³,王兆官^1,^2,³,齐浩^1,^2,^3,^*(

)

1 天津大学化工学院天津 300072
2 系统生物工程教育部重点实验室天津 300072
3 天津化学化工协同创新中心合成生物学平台天津 300072

Progress in Incorporation of Non-canonical Amino Acid Based on Archaeal Tyrosyl-tRNA Synthetase

HUANG Huan-bang^1,^2,³,WU Yang^1,^2,³,YANG You-hui^1,^2,³,WANG Zhao-guan^1,^2,³,QI Hao^1,^2,^3,^*(

)

1 School of Chemical Engineering and Technology, Tianjin 300072,China
2 Key Laboratory of Systems Bioengineering of Ministry of Education, Tianjin 300072,China
3 Syn Bio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin 300072,China

全文: PDF(2008 KB) HTML

摘要：

构筑蛋白质的编码信息存在于高度保守的密码子表中,而生物体仅利用20种天然氨基酸,就能排列组合出不同的蛋白质来行使多种生物学功能。通过合成生物学的飞速发展,使得在蛋白质合成中可控地引入非天然氨基酸成为可能。这极大地拓展了蛋白质的结构和功能,并为生物学工具的开发和生物生理过程的研究提供了便利。具有活性基团的非天然氨基酸可以广泛地应用于蛋白质结构研究、蛋白质功能调控以及新型生物材料构建和医药研发等诸多领域。基因密码子拓展技术利用正交翻译系统,通过重新分配密码子改造中心法则,可以在蛋白质的指定位点引入非天然氨基酸。系统地介绍了目前提升密码子拓展技术插入非天然氨基酸效率的方法,包括tRNA以及氨酰tRNA合成酶的各种突变方法和翻译辅助因子的改造。汇总了利用古细菌酪氨酰tRNA合成酶插入的非天然氨基酸和突变位点并总结了密码子拓展技术在生物医药领域的前沿进展。最后讨论了该项技术目前所面临的挑战,如可利用的密码子数量不多、正交翻译系统的种类有限和非天然氨基酸多插效率低下。希望能够帮助研究者建立适合的非天然氨基酸插入方法并推动密码子拓展技术进一步发展。

关键词： 密码子拓展; 非天然氨基酸; 生物正交; 合成生物学; 计算机辅助设计

Abstract:

The coding information used to build proteins exists in highly conserved codon table. In nature, organisms use 20 native amino acids to synthesize proteins of different lengths and orders to perform a variety of biological functions. In recent years, with the rapid development of synthetic biology, it is possible to controllably direct incorporation of non-canonical amino acids in protein synthesis. Non-canonical amino acids with functional side groups could extremely expand the structure and function of proteins, which could also be of benefit in the research of new synthetic biological tools and biological processes. The diversity of side chains serves in many fields, such as protein structure research, functional regulation, constructions of new bio-materials and bio-pharmaceutical industry development. This paper introduces the basic principle of the genetic codon expansion technology, and organizes the efficiency optimization strategies as well as new methods of constructing mutant library. In addition, it also summarizes the cutting-edge progress of the codon expansion technology in the field of bio-medicine. Finally, we summarize the current challenges faced by this technology, such as the limited number of available codons, the limited variety of orthogonal translation systems, and the low efficiency of multiple-incorporation of unnatural amino acids. We hope that these contents could help researchers establish suitable methods for the insertion of unnatural amino acids and promote the further development of this technology.

Key words: Genetic code expansion Non-canonical amino acid Bio-orthogonal Synthetic biology Computer-aided design

收稿日期: 2021-04-26 出版日期: 2021-09-30

ZTFLH:

Q819

通讯作者: 齐浩 E-mail: haoq@tju.edu.cn

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引用本文:

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.

HUANG Huan-bang,WU Yang,YANG You-hui,WANG Zhao-guan,QI Hao. Progress in Incorporation of Non-canonical Amino Acid Based on Archaeal Tyrosyl-tRNA Synthetase. China Biotechnology, 2021, 41(9): 110-125.

链接本文:

https://manu60.magtech.com.cn/biotech/CN/10.13523/j.cb.2104047 或 https://manu60.magtech.com.cn/biotech/CN/Y2021/V41/I9/110

图1 密码子拓展技术

图2 新型aaRS改造方法

图3 利用MjTyrRS/tRNA正交对插入的非天然氨基酸

图4 MjTyrRS突变频次统计

图5 非天然氨基酸在生化领域的应用

氨基酸序号		氨基酸名称	Mj TyrRS突变位点		年份	DOI
1		4-Propargyloxy-l-phenylalanine(pPR)	Y32L,D158S,I159M,L162K,A167H		2021	10.1002/cbic.202000663
2		4-(Trimethylsilyl)phenylalanine (TMSiPhe)	Y32H,I63G,L65V,H70Q,D158G,I159G,V164G		2020	10.1038/s41467-020-18433-5
3		3-Nitro-tyrosine	Y32H,L65L,H70T,D158H,I159A,L162R		2020	10.1016/j.jmb.2020.06.014
4		β-(1-azulenyl)-l-alanine (AzAla)	Y32A,L65W,H70G,F108H,Q109N,D158A,L162N		2019	10.1002/anie.201812995
5		Ortho-nitrobenzyl-tyrosine (ONBY)	Y32A,L65A,H70N,G105Q,Q109A,D158S,I159A,L162A,A167S,A180Q,D286R		2019	10.3390/ijms20092343
6		p-boronophenylalanine (Bpa)	Y32S,L65A,H70M,D158S,L162E,D286R		2018	10.1021/acs.biochem.8b00171
7		Biphenylalanine (BipA)	Y32H,D61V,L65H,H70Q,F108W,Q109M,D158G,L162K		2018	10.1073/pnas.1715137115
8		p-Iodo-L-phenylalanine (pIF)	Y32L,L69F,E107S,D158P,I159L,L162E,V235I		2017	10.1038/nCHeMBIO.2474
9		p-Nitro-L-phenylalanine (pNF)	Y32L,E107S,D158P,I159L,H160N,L162E		2017	10.1038/nCHeMBIO.2474
10		4-Phosphomethyl-L-phenylalanine (Pmp)	Y32L,L65A,F108K,Q109H,D158G,L162K		2017	10.1038/nchembio.2405
11		o-Phosphotyrosine (pTyr)	Y32L,L65A,F108K,Q109H,D158G,L162K		2017	10.1038/nchembio.2405
12		p-Acetyl-L-phenylalanine	Y32L,D158G,I159C,L162R,A167D,R257G (pAcFRS.1.t1)		2015	10.1038/nbt.3372
13		p-Azido-L-phenylalanine	Y32T,E107T,F108Y,Q109M,D158P,L162Q,R257G(pAzFRS.2.t1)		2015	10.1038/nbt.3372
氨基酸序号		氨基酸名称	Mj TyrRS突变位点		年份	DOI
14		4-(2'-Bromoisobutyramido)- phenylalanine (BibaF)	Y32G,L65E,F108W,Q109M,D158S,L162K		2014	10.1002/cbic.201402180
15		4-Transcycloocten-amidopheylalanine (Tco-amF)	Y32G,L65E,F108W,Q109M,D158S,L162K		2014	10.1002/cbic.201402180
16		Acridon-2-ylalanine (Acd)	Y32G,L65E,F108W,Q109M,D158S,L162K		2014	10.1002/cbic.201402180
17		4-Acetamidopheylalanine (AmF)	Y32G,L65E,F108W,Q109M,D158S,L162K		2014	10.1002/cbic.201402180
18		4-(6-Methyl-s-tetrazine-3-yl) aminophenylalanine (Tet-F)	Y32G,L65E,F108W,Q109M,D158S,L162K		2014	10.1002/cbic.201402180
19		4-Aminophenylalanine (AF)	Y32G,L65E,F108W,Q109M,D158S,L162K		2014	10.1002/cbic.201402180
20		4-Bromoisobutyryloxymethyl-l-phenylalanine (BiF)	Y32G,L65E,F108W,Q109M,D158S,L162K		2014	10.1002/cbic.201402180
21		4-Benzoyl-phenylalanine (Bpa)	Y32G,L65E,F108W,Q109M,D158S,L162K		2014	10.1002/cbic.201402180
22		o-Benzyl-L-tyrosine	Y32G,L65E,F108W,Q109M,D158S,L162K		2014	10.1002/cbic.201402180
23		p-Acrylamido-(S)-L-phenylalanine (AcrF)	Y32V,L65Y,F108H,Q109G,D158G,L162E,D286R		2014	10.1021/ja502851h
24		p-Vinylsulfonamido -(S)-L- phenylalanine (VSF)	Y32G,L65Y,F108H,Q109G,D158G,I159L,L162Q,D286R		2014	10.1021/ja502851h
25		2-Amino-3-(6-hydroxy-2-naphthyl)-propanoic acid (NpOH)	Y32E,L65T,D158S,I159A,H160P,Y161T,L162Q,A167W,D286R		2013	10.1021/bc400168u
26		7-MethylCoumarinyl-ethylGly	Y32E,L65H,A67G,H70G,F108Y,Q109H,D158G,L162G		2011	10.1021/ja106416g
27		p-(2-Tetrazole)-L-phenylalanine	Y32I,L65I,Q109M,D158G,L162V,V164G		2010	10.1021/ja104350y
28		o-Nitrobenzyl-2,6-difluoro-L-tyrosine	Y32G,L65G,H70M,F108G,D158S,I159M,L162E		2010	10.1021/bi100013s
29		o-Nitrobenzyl-3-difluoro-L-tyrosine	Y32G,L65G,H70N,F108G,D158S,I159M,L162N		2010	10.1021/bi100013s
30		o-Nitrobenzyl-2-difluoro-L-tyrosine	Y32G,L65G,H70N,F108G,D158S,I159M,L162N		2010	10.1021/bi100013s
31		p-Ethynyl-L-phenylalanine	Y32L,L65V,F108W,Q109M,D158G,I159P		2009	10.1021/bi900426d
32		2-Nitro-l-L-phenylalanine	Y32G,L65H,A67G,H70G,F108L,Q109S,Y114S,D158T,I159Y,L162D		2009	10.1016/j.chembiol.2009.01.013
33		Thyronine	A31V,Y32G,E107P,D158S,I159S		2009	10.1039/b904032c
34		3-Fluoro-4-nitro-p-benzoyl-L-phenylalanine(3F-4nitro-Bpa)	Y32G,E107P,D158T,I159S,V164A		2009	10.1039/b904032c
35		4-Nitro-p-benzoyl-L-phenylalanine(4Nitro-Bpa)	Y32G,E107P,D158T,I159S,V164A		2009	10.1039/b904032c
36		4-Iodo-p-benzoyl-L-phenylalanine(4I-Bpa)	Y32G,E107P,D158T,I159S,V164A		2009	10.1039/b904032c
37		2,6-Difluoro-p-benzoyl-L- phenylalanine (2,6dF-Bpa)	Y32G,E107P,D158T,I159S		2009	10.1039/b904032c
38		4-Fluoro-p-benzoyl-L-henylalanine(4F-Bpa)	A31V,Y32G,E107P,D158S,I159S		2009	10.1039/b904032c
39		p-Benzoyl-L-Phenylalanine(p-Bpa)	A31V,Y32G,E107P,D158S,I159S		2009	10.1039/b904032c
40		HQ-Ala	Y32V,L65M,H70T,F108R,Q109E,D158S,I159S		2009	10.1021/ja808340b
41		3-Iodo-L-tyrosine	H70A,D158T		2009	10.1016/j.str.2009.01.008
氨基酸序号		氨基酸名称	Mj TyrRS突变位点		年份	DOI
42	p-Cynao-L-phenylalanine			Y32L,L65V,F108W,Q109M,D158G,I159P	2009		10.1021/bi900426d
43	p-OCF₃-Phe			Y32A,L65S,F108Q,H109A,D158A,L162Y	2008		10.1021/ja801602q
44	3-Nitro-L-tyrosine			Y32R,L65L,H70L,Q23162M,D158G,I159L,L162H	2008		10.1021/ja710100d
45	PhenylselenoCys			Y32L,A67S,H70N,A167Q	2007		10.1002/ange.200702305
46	(2,2'-Bipyridin-5-yl) Ala(BpyAla)			Y32G,L65Y,H70A,F108F,Q109Q,Q155E,D158G,I159W,L162S	2007		10.1002/anie.200703397
47	3-Amino-L-tyrosine (NH2Y)			Y32Q,L65E,F108G,Q109L,L162Y	2007		10.1021/ja076043y
48	p-Carboxymethyl-L-phenylalanine (pCMF)			Y32S,L65A,F108K,Q109H,D158G,L162K	2007		10.1021/cb700083w
49	TfmdPhe			Y32I,H70F,E107S,Q109M,D158P,I159L,L162E	2007		10.1002/cbic.200700460
50	Sulfo-L-tyrosine			Y32L,L65P,D158G,I159C,L162K	2006		10.1038/nbt1254
51	Phe-4'-azobenzene (AzoPhe)			Y32G,L65E,F108A,Q109E,D158G,L162H	2006		10.1021/ja055467u
52	pAMF			Y32T,E107T,D158P,I159L,L162A	2006		10.1021/ja061099y
53	p-Methyl-L-phenylalanine			Y32L,L65A,F108S,H109H,D158A,L162M	2006		10.1021/ja061099y
54	(7-Hydroxycoumarin-4-yl)ethylGly			Y32E,L65H,A67G,H70G,F108Y,Q109H,D158G,L162G	2006		10.1021/ja062666k
55	m-Acetyl-L-phenylalanine			Y32L,D158E,I159P,H160Q,Y161G,L162R,G163D	2003		10.1021/bi0300231
56	3,4-Hydroxyl-L-phenylalanine			Y32L,A67S,H70N,A167Q	2003		10.1021/ja038242x
57	p-Isopropyl-L-phenylalanine			Y32G,T102C,V103A,E107P,D158G,I159Y	2002		10.1038/nbt742
58	O-Allyl-L-tyrosine			Y32S,E107T,D158T,I159Y,L162A	2002		10.1038/nbt742
59	3-(2-Naphthyl)-L-alanine			Y32L,D158P,I159A,L162Q,A167V	2002		10.1021/ja012307j
60	p-Methoxyl-L-phenylalanine			Y32Q,D158A,E107T,L162P	2001		10.1126/science.1060077

表S1 非天然氨基酸结构及其突变位点

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