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中国生物工程杂志

China Biotechnology
China Biotechnology
China Biotechnology  2021, Vol. 41 Issue (9): 110-125    DOI: 10.13523/j.cb.2104047
    
Progress in Incorporation of Non-canonical Amino Acid Based on Archaeal Tyrosyl-tRNA Synthetase
HUANG Huan-bang1,2,3,WU Yang1,2,3,YANG You-hui1,2,3,WANG Zhao-guan1,2,3,QI Hao1,2,3,*()
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
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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     
Received: 26 April 2021      Published: 30 September 2021
ZTFLH:  Q819  
Corresponding Authors: Hao QI     E-mail: haoq@tju.edu.cn
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Huan-bang HUANG
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Hao QI
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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.

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

Fig.1 Schematic of expanded genetic code methodology (a) Endogenous translation system in E. coli: AaRS charge its cognate tRNA with AA and then AA-tRNA complex is transferred to ribosome by elongation factor Tu (EF-Tu), where class I release factor (RF1) recognize stop codon and terminate the protein synthesis (b) Methodology of genetic code expansion: ncAA incorporation in response to amber codon is by means of o-aaRS/tRNA pair. The suppression efficiency is impeded by competition of RF1 (c) Genome manipulation of RF1 knock-out (d) Improved OTS includes evolved and optimized aaRS/tRNA pair and modified EF-Tu. The nonsense suppression efficiency is enhanced by RF1-depletion strain or orthogonal ribosome with mutant 16S rRNA
Fig.2 Novel methods for aaRS engineering (a) Multiplex automated genome engineering (b) Phage-assisted continuous evolution
Fig.3 Non-canonical amino acids that have been genetically encoded in proteins via MjTyrRS/tRNA pair The red box indicates that the amino acids contain -NO2 group, while the green, yellow, red and gray one is in response to halogen (F, Cl, Br, I), hydroxyl, primary or secondary amine and cyano or alkynyl
Fig.4 Mutation frequency statistics of MjTyrRS (a) Sites of mutation in response to protein structure (PDB:1J1U) in the circles indicate the position and the size correlate to the frequency of mutations. The mutant positions in the structure are colored red (b) The individual mutation of each site whose frequency are more than 3 times is shown in stack histogram
Fig.5 Application of protein bearing ncAAs in biology
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
Table S1 Structures of ncAAs and corresponding mutations
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