
ExpressInHost: A Codon Tuning Tool for the Expression of Recombinant Proteins in Host Microorganisms
References
- Burnett MJB, Burnett AC. “Therapeutic recombinant protein production in plants: Challenges and opportunities”. Plants People Planet. 2020; 2: 121–132. DOI: 10.1002/ppp3.10073
- Baeshen NA, Baeshen MN, Sheikh A, Bora RS, Ahmed MMM, Ramadan HAI, Saini KS, Redwan EM. “Cell factories for insulin production”. Microb Cell Factories. 2014; 13: 141. DOI: 10.1186/s12934-014-0141-0
- Kieliszek M, Misiewicz A. “Microbial transglutaminase and its application in the food industry”. Folia Microbiol. 2014; 59: 241–250. DOI: 10.1007/s12223-013-0287-x
- Jagadevan S, Banerjee A, Banerjee C, Guria C, Tiwari R, Baweja M, Shukla P. “Recent developments in synthetic biology and metabolic engineering in microalgae towards biofuel production”. Biotechnology for Biofuels. 2018; 11: 185. DOI: 10.1186/s13068-018-1181-1
- Rosano GL, Ceccarelli EA. “Recombinant protein expression in Escherichia coli: advances and challenges”. Front. Microbiol. 2014; 5: 172. DOI: 10.3389/fmicb.2014.00172
- GenSmart Design by GenScript
https://www.genscript.com/gene-and-plasmid-construct-design.html . - Genewiz by Brooks Life Sciences
https://www.genewiz.com/en-GB/Public/Services/Gene-Synthesis/codon-optimization . - Puigbò P, Guzmán E, Romeu A, Garcia-Vallvé S. “OPTIMIZER: a web server for optimizing the codon usage of DNA sequences”. Nucleic acids research. 2007; 35(Web Server issue); W126–31. DOI: 10.1093/nar/gkm219
- Condon A, Thachuk C. “Efficient codon optimization with motif engineering”. Journal of Discrete Algorithms. 2012; 16: 104–112. DOI: 10.1016/j.jda.2012.04.017
- Satya RV, Mukherjee A, Ranga U. “A pattern matching algorithm for codon optimization and CpG motif- engineering in DNA expression vectors”. Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003. 2003; 294–305. DOI: 10.1109/CSB.2003.1227330
- Huang Y, Lin T, Lu L, Cai F, Lin J, Jiang Y, Lin Y. “Codon pair optimization (CPO): a software tool for synthetic gene design based on codon pair bias to improve the expression of recombinant proteins in Pichia pastoris”. Microbial Cell Factories. 2021; 20: 209. DOI: 10.1186/s12934-021-01696-y
- Fuglsang A. “Codon optimizer: a freeware tool for codon optimization”. Protein Expression and Purification. 2003; 31(2): 247–249. DOI: 10.1016/S1046-5928(03)00213-4
- Gould N, Hendy O, Papamichail D. “Computational tools and algorithms for designing customized synthetic genes”. Front. Bioeng. Biotechnol. 2014; 2: 41. DOI: 10.3389/fbioe.2014.00041
- Watts A, Sankaranarayanan S, Watts A, Raipuria RK. “Optimizing protein expression in heterologous system: Strategies and tools”. Meta Gene. 2021; 29: 100899. DOI: 10.1016/j.mgene.2021.100899
- dos Reis M, Savva R, Wernisch L. “Solving the riddle of codon usage preferences: a test for translational selection”. Nucleic Acids Res. 2004; 32(17): 5036–5044. DOI: 10.1093/nar/gkh834
- Sharp PM, Li WH. “The codon Adaptation Index–a measure of directional synonymous codon usage bias, and its potential applications”. Nucleic Acids Res. 1987; 15(3): 1281–1295. DOI: 10.1093/nar/15.3.1281
- Ikemura T. “Codon usage and tRNA content in unicellular and multicellular organisms”. Mol. Biol. Evol. 1985; 2(1): 13–34. DOI: 10.1093/oxfordjournals.molbev.a040335
- Ikemura T. “Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes”. J. Mol. Biol. 1981; 146(1): 1–21. DOI: 10.1016/0022-2836(81)90363-6
- Ikemura T. “Correlation between the abundance of yeast transfer RNAs and the occurrence of the respective codons in protein genes. Differences in synonymous codon choice patterns of yeast and Escherichia coli with reference to the abundance of isoaccepting transfer RNAs”. J. Mol. Biol. 1982; 158(4): 573–597. DOI: 10.1016/0022-2836(82)90250-9
- Gouy M, Gautier C. “Codon usage in bacteria: correlation with gene expressivity”. Nucleic Acids Res. 1982; 10(22): 7055–7074. DOI: 10.1093/nar/10.22.7055
- Bennetzen JL, Hall BD. “Codon selection in yeast”. J. Biol. Chem. 1982; 257(6): 3026–3031. DOI: 10.1016/S0021-9258(19)81068-2
- Ignatova Z, Narberhaus F. “Systematic probing of the bacterial RNA structurome to reveal new functions”. Curr. Opin. Microbiol. 2017; 36: 14–19. DOI: 10.1016/j.mib.2017.01.003
- Rauscher R, Ignatova Z. “Timing during translation matters: synonymous mutations in human pathologies influence protein folding and function”. Biochemical Society Transactions, 2018; 46(4): 937–944. DOI: 10.1042/BST20170422
- Ciandrini L, Stansfield I, Romano MC. “Ribosome traffic on mRNAs maps to gene ontology: genome-wide quantification of translation initiation rates and polysome size regulation”. PLoS Comput. Biol., 2013; 9(1):
e1002866 . DOI: 10.1371/journal.pcbi.1002866 - Brackley CA, Romano MC, Thiel M. “The dynamics of supply and demand in mRNA translation”. PLoS Comput. Biol, 2011; 7(10):
e1002203 . DOI: 10.1371/journal.pcbi.1002203 - McFarland MR, Keller CD, Childers BM, Adeniyi SA, Corrigall H, Raguin A, Romano MC, Stansfield I. “The molecular aetiology of tRNA synthetase depletion: induction of a GCN4 amino acid starvation response despite homeostatic maintenance of charged tRNA levels”. Nucleic acids research, 2020; 48(6): 3071–3088. DOI: 10.1093/nar/gkaa055
- Percudani R, Pavesi A, Ottonello S. “Transfer RNA gene redundancy and translational selection in Saccharomyces cerevisiae”. J. Mol. Biol. 1997; 268: 322–330. DOI: 10.1006/jmbi.1997.0942
- Gilchrist MA, Wagner A. “A model of protein translation including codon bias, nonsense errors, and ribosome recylcing”. J. Theor. Biol. 2006; 239(4): 417–34. DOI: 10.1016/j.jtbi.2005.08.007
- Grosjean H, de Crécy-Lagard V, Marck C. “Deciphering synonymous codons in the three domains of life: Co-evolution with specific tRNA modification enzymes”. FEBS letters. 2010; 584: 252–264. DOI: 10.1016/j.febslet.2009.11.052
- Kirchner S, Cai Z, Rauscher R, Kastelic N, Anding M, Czech A, Kleizen B, Ostedgaard LS, Braakman I, Sheppard DN, Igntova Z. “Alteration of protein function by a silent polymorphism linked to tRNA abundance”. PLoS Biol. 2017; 15:
e2000779 . DOI: 10.1371/journal.pbio.2000779 - Kimchi-Sarfaty C, Oh JM, Kim IW, Sauna ZE, Calcagno AM, Ambudkar SV, Gottesman MM. “A ‘silent’ polymorphism in the MDR1 gene changes substrate specificity”. Science. 2007; 315(5811): 525–528. DOI: 10.1126/science.1135308
- Simhadri VL, Hamasaki-Katagiri N, Lin BC, Hunt R, Jha S, Tseng SC, Wu A, Bentley AA, Zichel R, Lu Q, Zhu L, Freedberg D, Monroe DM, Sauna ZE, Peters R, Komar AA, Kimchi-Sarfaty C. “Single synonymous mutation in factor IX alters protein properties and underlies haemophilia B”. J. Med. Genet. 2017; 54: 338–345. DOI: 10.1136/jmedgenet-2016-104072
- Fredrick K, Ibba M. “How the sequence of a gene can tune its translation”. Cell. 2010; 141: 227–229. DOI: 10.1016/j.cell.2010.03.03321
- Jacobson GN, Clark PL. “Quality over quantity: optimizing co-translational protein folding with non-‘optimal’ synonymous codons”. Curr. Opin. Struct. Biol. 2016; 38: 102–110. DOI: 10.1016/j.sbi.2016.06.00222
- Pechmann S, Chartron JW, Frydman J. “Local slowdown of translation by nonoptimal codons promotes nascent-chain recognition by SRPin vivo”. Nat. Struct. Mol. Biol. 2014; 21: 1100–1105. DOI: 10.1038/nsmb.291923
- Zhang G, Ignatova Z. “Folding at the birth of the nascent chain: coordinating translation with co-translational folding”. Curr. Opin. Struct. Biol. 2011; 21: 25–31. DOI: 10.1016/j.sbi.2010.10.008
- Chaney JL, Steele A, Carmichael R, Rodriguez A, Specht AT, Ngo K, Li J, Emrich S, Clark PL. “Widespread position-specific conservation of synonymous rare codons within coding sequences”. PLoS Comput. Biol. 2017; 13:
e1005531 DOI: 10.1371/journal.pcbi.1005531 - Zhang G, Ignatova Z. “Generic algorithm to predict the speed of translational elongation: implications for protein biogenesis”. PLoS ONE. 2009; 4(4),
e5036 . DOI: 10.1371/journal.pone.0005036 - Lopinski JD, Dinman JD, Bruenn JA. “Kinetics of Ribosomal Pausing during Programmed –1 Translational Frameshifting”. Mol. Cell. Biol. 2000; 20(4): 1095–1103. DOI: 10.1128/MCB.20.4.1095-1103.2000
https://www.ebi.ac.uk/Tools/msa/clustalo/ .
DOI: https://doi.org/10.5334/jors.385 | Journal eISSN: 2049-9647
Language: English
Submitted on: Jul 19, 2021
Accepted on: Sep 16, 2022
Published on: Feb 1, 2023
Published by: Ubiquity Press
In partnership with: Paradigm Publishing Services
Publication frequency: 1 issue per year
© 2023 Adélaïde Raguin, Ian Stansfield, Maria Carmen Romano, published by Ubiquity Press
This work is licensed under the Creative Commons Attribution 4.0 License.