Please wait a minute...

中国生物工程杂志

China Biotechnology
China Biotechnology  2021, Vol. 41 Issue (4): 64-73    DOI: 10.13523/j.cb.2101004
    
Progress in the Study of Microbial tRNA and Genetic Codon System Related Applications
LIAO Dan-ni,ZHANG Zhao-yang,JIN Jin,LI Xia,JIA Bin()
Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, China
Download: HTML   PDF(11248KB) HTML
Export: BibTeX | EndNote (RIS)      

Abstract  

The tRNA are important molecules of the translation process in the central dogma of life. The type and abundance of tRNA have a huge impact on the synthesis of proteins. In recent years, many inspirations have been obtained through the analysis of the structure and function of microbial tRNA and the process of tRNA modification. Moreover, the study of genetic codon expansion has realized the incorporation of unnatural amino acids into specific positions to obtain new functional proteins. At the same time, the codon recoding work carried out through chemical synthesis of microbial genomes will release more codons and tRNAs for more genetic codon expansion research. This work reviewed the latest application research progress of microbial tRNA and codon system in synthetic biology, and discussed the future development trend.



Key wordstRNA      Genetic codon expansion      Unnatural amino acid      Aminoacyl tRNA synthetase     
Received: 04 January 2021      Published: 30 April 2021
ZTFLH:  Q819  
Corresponding Authors: Bin JIA     E-mail: bin.jia@tju.edu.cn
Cite this article:

LIAO Dan-ni,ZHANG Zhao-yang,JIN Jin,LI Xia,JIA Bin. Progress in the Study of Microbial tRNA and Genetic Codon System Related Applications. China Biotechnology, 2021, 41(4): 64-73.

URL:

https://manu60.magtech.com.cn/biotech/10.13523/j.cb.2101004     OR     https://manu60.magtech.com.cn/biotech/Y2021/V41/I4/64

Fig.1 Study of tRNA and genetic codon system related applications (a) tRNA secondary structure (b) Generation of multiple gRNAs by using the endogenous tRNA processing system (c) Transcription of tRNA genes by RNA polymerase III (d) Suppressor tRNA interact with cognate orthogonal aminoacyl-tRNA synthetases (o-aaRSs) and host aaRS (e) Directed evolution of aaRS (f) Construction of molecular switch with ncAA
[1]   Hopper A K, Phizicky E M. tRNA transfers to the limelight. Genes & Development, 2003,17(2):162-180.
[2]   Goodenbour J M, Pan T. Diversity of tRNA genes in eukaryotes. Nucleic Acids Research, 2006,34(21):6137-6146.
[3]   冯德江, 刘翔, 李旭刚, 等. tRNA丰度与基因表达的关系. 中国生物工程杂志, 2002,22(6):4-8.
[3]   Feng D J, Liu X, Li X G, et al. The relationship between tRNA abundance and gene expression. China Biotechnology, 2002,22(6):4-8.
[4]   Konopka A K. Theory of degenerate coding and informational parameters of protein coding genes. Biochimie, 1985,67(5):455-468.
pmid: 4027279
[5]   Konopka A K, Brendel V. The missense errors in protein can be controlled by selective synonymous codon usage at the level of transcription. Biochimie, 1985,67(5):469-473.
pmid: 2992612
[6]   杨云彭, 马晓焉, 霍毅欣. 密码子优化策略在异源蛋白表达中的应用. 生物工程学报, 2019,35(12):2227-2237.
[6]   Yang Y P, Ma X Y, Huo Y X. Application of codon optimization strategy in heterologous protein expression. Chinese Journal of Biotechnology, 2019,35(12):2227-2237.
[7]   Phizicky E M, Hopper A K. tRNA biology charges to the front. Genes & Development, 2010,24(17):1832-1860.
pmid: 20810645
[8]   Giegé R, Jühling F, Pütz J, et al. Structure of transfer RNAs: similarity and variability. Wiley Interdisciplinary Reviews: RNA, 2012,3(1):37-61.
doi: 10.1002/wrna.103 pmid: 21957054
[9]   Jakubowski H. Quality control in tRNA charging. Wiley Interdisciplinary Reviews: RNA, 2012,3(3):295-310.
[10]   Wellner K, Betat H, Mörl M. A tRNA’s fate is decided at its 3' end: Collaborative actions of CCA-adding enzyme and RNases involved in tRNA processing and degradation. Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, 2018,1861(4):433-441.
[11]   Hopper A K. Transfer RNA post-transcriptional processing, turnover, and subcellular dynamics in the yeast Saccharomyces cerevisiae. Genetics, 2013,194(1):43-67.
[12]   Raina M, Ibba M. tRNAs as regulators of biological processes. Frontiers in Genetics, 2014,5:171-185.
[13]   Cong L, Ran F A, Cox D, et al. Multiplex genome engineering using CRISPR/Cas systems. Science, 2013,339(6121):819-823.
doi: 10.1126/science.1231143 pmid: 23287718
[14]   Mali P, Yang L H, Esvelt K M, et al. RNA-guided human genome engineering via Cas9. Science, 2013,339(6121):823-826.
pmid: 23287722
[15]   Wang H Y, Yang H, Shivalila C S, et al. One-step generation of mice carrying mutations in multiple genes by CRISPR/cas-mediated genome engineering. Cell, 2013,153(4):910-918.
[16]   Shan Q W, Wang Y P, Li J, et al. Targeted genome modification of crop plants using a CRISPR-Cas system. Nature Biotechnology, 2013,31(8):686-688.
doi: 10.1038/nbt.2650 pmid: 23929338
[17]   Xie K B, Minkenberg B, Yang Y N. Boosting CRISPR/Cas9 multiplex editing capability with the endogenous tRNA-processing system. Proceedings of the National Academy of Sciences of the United States of America, 2015,112(11):3570-3575.
[18]   Vargas-Rodriguez O, Sevostyanova A, Söll D, et al. Upgrading aminoacyl-tRNA synthetases for genetic code expansion. Current Opinion in Chemical Biology, 2018,46:115-122.
pmid: 30059834
[19]   Chin J W. Expanding and reprogramming the genetic code of cells and animals. Annual Review of Biochemistry, 2014,83:379-408.
[20]   Mukai T, Lajoie M J, Englert M, et al. Rewriting the genetic code. Annual Review of Microbiology, 2017,71:557-577.
[21]   Hoffman K, Crnković A, Söll D. Versatility of synthetic tRNAs in genetic code expansion. Genes, 2018,9(11):537-552.
[22]   Giegé R, Sissler M, Florentz C. Universal rules and idiosyncratic features in tRNA identity. Nucleic Acids Research, 1998,26(22):5017-5035.
doi: 10.1093/nar/26.22.5017 pmid: 9801296
[23]   Kisselev L L. The role of the anticodon in recognition of tRNA by aminoacyl-tRNA synthetases. Progress in Nucleic Acid Research and Molecular Biology, 1985,32:237-266.
[24]   Melnikov S V, Söll D. Aminoacyl-tRNA synthetases and tRNAs for an expanded genetic code: what makes them orthogonal? International Journal of Molecular Sciences, 2019,20(8):1929-1935.
[25]   Senger B, Auxilien S, Englisch U, et al. The modified wobble base inosine in yeast tRNAIle is a positive determinant for aminoacylation by isoleucyl-tRNA synthetase. Biochemistry, 1997,36(27):8269-8275.
doi: 10.1021/bi970206l pmid: 9204872
[26]   Normanly J, Kleina L G, Masson J M, et al. Construction of Escherichia coli amber suppressor tRNA genes: III. Determination of tRNA specificity. Journal of Molecular Biology, 1990,213(4):719-726.
pmid: 2141650
[27]   McClain W H, Foss K, Jenkins R A, et al. Nucleotides that determine Escherichia coli tRNA(Arg) and tRNA(Lys) acceptor identities revealed by analyses of mutant opal and amber suppressor tRNAs. PNAS, 1990,87(23):9260-9264.
pmid: 2251270
[28]   Sylvers L A, Rogers K C, Shimizu M, et al. A 2-thiouridine derivative in tRNAGlu is a positive determinant for aminoacylation by Escherichia coli glutamyl-tRNA synthetase. Biochemistry, 1993,32(15):3836-3841.
[29]   Muramatsu T, Nishikawa K, Nemoto F, et al. Codon and amino-acid specificities of a transfer RNA are both converted by a single post-transcriptional modification. Nature, 1988,336(6195):179-181.
pmid: 3054566
[30]   Pütz J, Florentz C, Benseler F, et al. A single methyl group prevents the mischarging of a tRNA. Nature Structural Biology, 1994,1(9):580-582.
pmid: 7634096
[31]   Schulman L H, Pelka H. Anticodon switching changes the identity of methionine and valine transfer RNAs. Science (New York, N Y), 1988,242(4879):765-768.
[32]   Steinfeld J B, Aerni H R, Rogulina S, et al. Expanded cellular amino acid pools containing phosphoserine, phosphothreonine, and phosphotyrosine. ACS Chemical Biology, 2014,9(5):1104-1112.
doi: 10.1021/cb5000532 pmid: 24646179
[33]   Galli G, Hofstetter H, Birnstiel M L. Two conserved sequence blocks within eukaryotic tRNA genes are major promoter elements. Nature, 1981,294:626-631.
[34]   Sharp S, DeFranco D, Dingermann T, et al. Internal control regions for transcription of eukaryotic tRNA genes. Proceedings of the National Academy of Sciences of the United States of America, 1981,78(11):6657-6661.
[35]   Reynolds N M, Vargas-Rodriguez O, Söll D, et al. The central role of tRNA in genetic code expansion. Biochimica et Biophysica Acta (BBA) - General Subjects, 2017,1861(11):3001-3008.
[36]   Drabkin H J, Park H J, Rajbhandary U L. Amber suppression in mammalian cells dependent upon expression of an Escherichia coli aminoacyl-tRNA synthetase gene. Molecular and Cellular Biology, 1996,16(3):907-913.
pmid: 8622693
[37]   Köhrer C, Xie L, Kellerer S, et al. Import of amber and ochre suppressor tRNAs into mammalian cells: a general approach to site-specific insertion of amino acid analogues into proteins. Proceedings of the National Academy of Sciences of the United States of America, 2001,98(25):14310-14315.
[38]   Sakamoto K, Hayashi A, Sakamoto A, et al. Site-specific incorporation of an unnatural amino acid into proteins in mammalian cells. Nucleic Acids Research, 2002,30(21):4692-4699.
[39]   Wang Q, Wang L. Genetic incorporation of unnatural amino acids into proteins in yeast. Methods in Molecular Bology (Clifton, N.J.), 2012,794:199-213.
[40]   Mukai T, Kobayashi T, Hino N, et al. Adding l-lysine derivatives to the genetic code of mammalian cells with engineered pyrrolysyl-tRNA synthetases. Biochemical and Biophysical Research Communications, 2008,371(4):818-822.
[41]   Hancock S M, Uprety R, Deiters A, et al. Expanding the genetic code of yeast for incorporation of diverse unnatural amino acids via a pyrrolysyl-tRNA synthetase/tRNA pair. Journal of the American Chemical Society, 2010,132(42):14819-14824.
pmid: 20925334
[42]   Shao N, Singh N S, Slade S E, et al. Site specific genetic incorporation of azidophenylalanine in Schizosaccharomyces pombe. Scientific Reports, 2015,5:17196.
pmid: 26597962
[43]   Machnicka M A, Olchowik A, Grosjean H, et al. Distribution and frequencies of post-transcriptional modifications in tRNAs. RNA Biology, 2014,11(12):1619-1629.
pmid: 25611331
[44]   Randau L, Münch R, Hohn M J, et al. Nanoarchaeum equitans creates functional tRNAs from separate genes for their 5'- and 3'-halves. Nature, 2005,433(7025):537-541.
doi: 10.1038/nature03233 pmid: 15690044
[45]   Berg M D, Hoffman K S, Genereaux J, et al. Evolving mistranslating tRNAs through a phenotypically ambivalent intermediate in Saccharomyces cerevisiae. Genetics, 2017,206(4):1865-1879.
doi: 10.1534/genetics.117.203232 pmid: 28576863
[46]   Tharp J M, Ehnbom A, Liu W R. tRNAPyl: Structure, function, and applications. RNA Biology, 2018,15(4-5):441-452.
pmid: 28837402
[47]   Wang K H, Neumann H, Peak-Chew S Y, et al. Evolved orthogonal ribosomes enhance the efficiency of synthetic genetic code expansion. Nature Biotechnology, 2007,25(7):770-777.
pmid: 17592474
[48]   Orelle C, Carlson E D, Szal T, et al. Protein synthesis by ribosomes with tethered subunits. Nature, 2015,524(7563):119-124.
pmid: 26222032
[49]   Fried S D, Schmied W H, Uttamapinant C, et al. Ribosome subunit stapling for orthogonal translation in E. coli. Angewandte Chemie, 2015,127(43):12982-12985.
pmid: 27570300
[50]   Mukai T, Hayashi A, Iraha F, et al. Codon reassignment in the Escherichia coli genetic code. Nucleic Acids Research, 2010,38(22):8188-8195.
pmid: 20702426
[51]   Dumas A, Lercher L, Spicer C D, et al. Designing logical codon reassignment - Expanding the chemistry in biology. Chemical Science, 2015,6(1):50-69.
pmid: 28553457
[52]   Wang Y S, Fang X Q, Chen H Y, et al. Genetic incorporation of twelve meta-substituted phenylalanine derivatives using a single pyrrolysyl-tRNA synthetase mutant. ACS Chemical Biology, 2013,8(2):405-415.
doi: 10.1021/cb300512r pmid: 23138887
[53]   Lajoie M J, Rovner A J, Goodman D B, et al. Genomically recoded organisms expand biological functions. Science, 2013,342(6156):357-360.
pmid: 24136966
[54]   Ostrov N, Landon M, Guell M, et al. Design, synthesis, and testing toward a 57-codon genome. Science, 2016,353(6301):819-822.
doi: 10.1126/science.aaf3639 pmid: 27540174
[55]   Richardson S M, Mitchell L A, Stracquadanio G, et al. Design of a synthetic yeast genome. Science, 2017,355(6329):1040-1044.
doi: 10.1126/science.aaf4557 pmid: 28280199
[56]   Fredens J, Wang K H, de la Torre D, et al. Total synthesis of Escherichia coli with a recoded genome. Nature, 2019,569(7757):514-518.
pmid: 31092918
[57]   Kavran J M, Gundllapalli S, O’Donoghue P, et al. Structure of pyrrolysyl-tRNA synthetase, an archaeal enzyme for genetic code innovation. Proceedings of the National Academy of Sciences of the United States of America, 2007,104(27):11268-11273.
[58]   Giegé R, Sissler M, Florentz C. Universal rules and idiosyncratic features in tRNA identity. Nucleic Acids Research, 1998,26(22):5017-5035.
doi: 10.1093/nar/26.22.5017 pmid: 9801296
[59]   Nozawa K, O’Donoghue P, Gundllapalli S, et al. Pyrrolysyl-tRNA synthetase-tRNA(Pyl) structure reveals the molecular basis of orthogonality. Nature, 2009,457(7233):1163-1167.
doi: 10.1038/nature07611 pmid: 19118381
[60]   Bullwinkle T, Lazazzera B, Ibba M. Quality control and infiltration of translation by amino acids outside of the genetic code. Annual Review of Genetics, 2014,48:149-166.
doi: 10.1146/annurev-genet-120213-092101 pmid: 25195507
[61]   Ruan B, Palioura S, Sabina J, et al. Quality control despite mistranslation caused by an ambiguous genetic code. Proceedings of the National Academy of Sciences of the United States of America, 2008,105(43):16502-16507.
[62]   Cowie D B, Cohen G N. Biosynthesis by Escherichia coli of active altered proteins containing selenium instead of sulfur. Biochimica et Biophysica Acta, 1957,26(2):252-261.
pmid: 13499359
[63]   Hendrickson W A, Horton J R, LeMaster D M. Selenomethionyl proteins produced for analysis by multiwavelength anomalous diffraction (MAD): a vehicle for direct determination of three-dimensional structure. The EMBO Journal, 1990,9(5):1665-1672.
pmid: 2184035
[64]   Dieterich D C, Hodas J J L, Gouzer G, et al. In situ visualization and dynamics of newly synthesized proteins in rat hippocampal neurons. Nature Neuroscience, 2010,13(7):897-905.
doi: 10.1038/nn.2580 pmid: 20543841
[65]   Gan Q L, Lehman B P, Bobik T A, et al. Expanding the genetic code of Salmonella with non-canonical amino acids. Scientific Reports, 2016,6:39920.
doi: 10.1038/srep39920 pmid: 28008993
[66]   He J X, Van Treeck B, Nguyen H B, et al. Development of an unnatural amino acid incorporation system in the actinobacterial natural product producer Streptomyces venezuelae ATCC 15439. ACS Synthetic Biology, 2016,5(2):125-132.
doi: 10.1021/acssynbio.5b00209 pmid: 26562751
[67]   Wang F, Robbins S, Guo J T, et al. Genetic incorporation of unnatural amino acids into proteins in Mycobacterium tuberculosis. PLoS One, 2010,5(2):e9354.
doi: 10.1371/journal.pone.0009354 pmid: 20179771
[68]   Haimovich A D, Muir P, Isaacs F J. Genomes by design. Nature Reviews Genetics, 2015,16(9):501-516.
[69]   Packer M S, Liu D R. Methods for the directed evolution of proteins. Nature Reviews Genetics, 2015,16(7):379-394.
doi: 10.1038/nrg3927 pmid: 26055155
[70]   Badran A H, Liu D R. Development of potent in vivo mutagenesis plasmids with broad mutational spectra. Nature Communications, 2015,6:8425.
doi: 10.1038/ncomms9425 pmid: 26443021
[71]   Suzuki T, Miller C, Guo L T, et al. Crystal structures reveal an elusive functional domain of pyrrolysyl-tRNA synthetase. Nature Chemical Biology, 2017,13(12):1261-1266.
doi: 10.1038/nchembio.2497 pmid: 29035363
[72]   Tian R Z, Liu Y F, Cao Y T, et al. Titrating bacterial growth and chemical biosynthesis for efficient N -acetylglucosamine and N -acetylneuraminic acid bioproduction. Nature Communications, 2020,11(1):5078.
doi: 10.1038/s41467-020-18960-1 pmid: 33033266
[73]   Huang S M, Yang F, Cai B Y, et al. Genetically encoded fluorescent amino acid for monitoring protein interactions through FRET. Analytical Chemistry, 2019,91(23):14936-14942.
doi: 10.1021/acs.analchem.9b03305 pmid: 31670502
[74]   Liu X H, Kang F Y, Hu C, et al. A genetically encoded photosensitizer protein facilitates the rational design of a miniature photocatalytic CO2-reducing enzyme. Nature Chemistry, 2018,10(12):1201-1206.
doi: 10.1038/s41557-018-0150-4 pmid: 30397317
[75]   Yu Y, Liu X H, Wang J Y. Expansion of redox chemistry in designer metalloenzymes. Accounts of Chemical Research, 2019,52(3):557-565.
doi: 10.1021/acs.accounts.8b00627 pmid: 30816694
[76]   Cervettini D, Tang S, Fried S D, et al. Rapid discovery and evolution of orthogonal aminoacyl-tRNA synthetase-tRNA pairs. Nature Biotechnology, 2020,38(8):989-999.
doi: 10.1038/s41587-020-0479-2 pmid: 32284585
[77]   Fischer E C, Hashimoto K, Zhang Y, et al. New codons for efficient production of unnatural proteins in a semisynthetic organism. Nature Chemical Biology, 2020,16(5):570-576.
doi: 10.1038/s41589-020-0507-z pmid: 32251411
[78]   Völler J S, Budisa N. Coupling genetic code expansion and metabolic engineering for synthetic cells. Current Opinion in Biotechnology, 2017,48:1-7.
pmid: 28237511
[79]   付宪, 林涛, 张帆, 等. 基因密码子拓展技术的方法原理和前沿应用研究进展. 合成生物学, 2020,1(1):103-119.
[79]   Fu X, Lin T, Zhang F, et al. Progress in the study of genetic code expansion related methods, principles and applications. Synthetic Biology Journal, 2020,1(1):103-119.
[1] HAN Yan, HUANG Yuan, YE Hai-yan. tRNase Z’s Research Progress[J]. China Biotechnology, 2012, 32(04): 110-116.
[2] ZHOU Qi-Hua-1, ZHOU Cheng-Mei-2. Research Progress on Aminoacyl-tRNA Synthetases[J]. China Biotechnology, 2009, 29(06): 130-134.