The Gene Sequence Optimization of Membrane Protein in Prokaryotic Expression System

doi:10.13560/j.cnki.biotech.bull.1985.2015.12.007

Abstract

Abstract: Studies of the structure and function of membrane proteins are hotspots of life science in recent years. The most important approach to acquire membrane protein is recombinant expression in prokaryotic system. However, the yield of membrane protein in prokaryotic system is relatively low. Gene sequence optimization is a effective technique to enhance expression of membrane protein in prokaryotic system. In this article, we summarize the latest progress on gene sequence optimization for the prokaryotic expression of membrane proteins, and discuss the factors which affect the expression of membrane protein, including the optimization of rare codons, mRNA stability and translation starting, mRNA and ribosome behaviour, translation rate and membrane protein folding. Our paper provides new possibilities for the over-expression of membrane protein in prokaryotic system.

Key words: membrane protein, over-expression, gene sequence optimization, rare codons optimization, mRNA stability, translation rate, membrane protein folding

Wang Shishan, Chen Yanke, Yang Jun. The Gene Sequence Optimization of Membrane Protein in Prokaryotic Expression System[J]. Biotechnology Bulletin, 2015, 31(12): 50-55.

References

[1]Yildirim MA, Goh KI, Cusick ME, et al. Drug-target network[J]. Nature Biotechnology, 2007, 25(10):1119-1126.
[2]Cross TA, Ekanayake V, Paulino J, et al. Solid state NMR:The essential technology for helical membrane protein structural characterization[J]. Journal of Magnetic Resonance, 2014, 239:100-109.
[3]Chen YK, Zhang ZF, Tang XQ, et al. Conformation and topology of diacylglycerol kinase in E. coli membranes revealed by solid-state NMR spectroscopy[J]. Angewandte Chemie-International Edition, 2014, 53(22):5624-5628.
[4]Su PC, Si W, Baker DL, et al. High-yield membrane protein expression from E. coli using an engineered outer membrane protein F fusion[J]. Protein Science, 2013, 22(4):434-443.
[5]Dong GF, Wang CZ, Wu YH, et al. Tat peptide-mediated soluble expression of the membrane protein LSECtin-CRD in Escherichia coli[J]. PLoS One, 2013, 8(12):e83579.
[6]Zuo X, Lie S, Hall J, et al. Enhanced expression and purification of membrane proteins by SUMO fusion in Escherichia coli[J]. Journal of Structural and Functional Genomics, 2005, 6(2-3):103-111.
[7]Guimaraes JC, Rocha M, Arkin AP. Transcript level and sequence determinants of protein abundance and noise in Escherichia coli[J]. Nucleic Acids Research, 2014, 42(8):4791-4799.
[8]Prilusky J, Bibi E. Studying membrane proteins through the eyes of the genetic code revealed a strong uracil bias in their coding mRNAs[J]. Proceedings of the National Academy of Sciences of the United States of America, 2009, 106(16):6662-6666.
[9]Norholm MHH, Light S, Virkki MTI, et al. Manipulating the genetic code for membrane protein production:what have we learnt so far?[J]. Biochimica Et Biophysica Acta-Biomembranes, 2012, 1818(4):1091-1096.
[10]Greenbaum D, Jansen R, Gerstein M. Analysis of mRNA expression and protein abundance data:an approach for the comparison of the enrichment of features in the cellular population of proteins and transcripts[J]. Bioinformatics, 2002, 18(4):585-596.
[11]Jansen R, Gerstein M. Analysis of the yeast transcriptome with structural and functional categories:characterizing highly expressed proteins[J]. Nucleic Acids Research, 2000, 28(6):1481-1488.
[12]Kimchi-Sarfaty C, Oh JM, Kim IW, et al. A "silent" polymorphism in the MDR1 gene changes substrate specificity[J]. Science, 2007, 315(5811):525-528.
[13]Kepes F. The"+70 pause":Hypothesis of a translational control of membrane protein assembly[J]. Journal of Molecular Biology, 1996, 262(2):77-86.
[14]Dessen P, Kepes F. The PAUSE software for analysis of translational control over protein targeting:application to E-nidulans membrane proteins[J]. Gene, 2000, 244(1-2):89-96.
[15]Katzen F, Peterson TC, Kudlicki W. Membrane protein expression:no cells required[J]. Trends in Biotechnology, 2009, 27(8):455-460.
[16]Wang Q, Mei C, Zhen HH, et al. Codon preference optimization increases prokaryotic cystatin C expression[J]. Journal of Biom-edicine and Biotechnology, 2012, doi:org/10.1155/2012/732017.
[17]Norholm MHH, Toddo S, Virkki MTI, et al. Improved production of membrane proteins in Escherichia coli by selective codon substitutions[J]. Febs Letters, 2013, 587(15):2352-2358.
[18]Grosjean H, Fiers W. Preferential codon usage in prokaryotic genes-the optimal codon anticodon interaction energy and the selective co-don usage in efficiently expressed genes[J]. Gene, 1982, 18(3):199-209.
[19]Gouy M, Gautier C. Codon usage in bacteria-correlation with gene expressivity[J]. Nucleic Acids Research, 1982, 10(22):7055-7074.
[20]L?w C, Jegersch?ld C, Kovermann M, et al. Optimisation of over-expression in E. coli and biophysical characterisation of human membrane protein synaptogyrin 1[J]. PLoS One, 2012, 7(6):e38244.
[21]Hardt B, Volker C, Mundt S, et al. Human endo-alpha 1, 2-mannosidase is a golgi-resident type II membrane protein[J]. Biochimie, 2005, 87(2):169-179.
[22]Hassan KA, Xu ZQ, Watkins RE, et al. Optimized production and analysis of the staphylococcal multidrug efflux protein QacA[J]. Protein Expression and Purification, 2009, 64(2):118-124.
[23]Slimko EM, Lester HA. Codon optimization of Caenorhabditis elegans GluCl ion channel genes for mammalian cells dramatically improves expression levels[J]. Journal of Neuroscience Methods, 2003, 124(1):75-81.
[24]Sohl CD, Guengerich FP. Kinetic Analysis of the three-step steroid aromatase reaction of human cytochrome P450 19A1[J]. Journal of Biological Chemistry, 2010, 285(23):17734-17743.
[25]Baneres JL, Martin A, Hullot P, et al. Structure-based analysis of GPCR function:conformational adaptation of both agonist and receptor upon leukotriene B-4 binding to recombinant BLT1[J]. Journal of Molecular Biology, 2003, 329(4):801-814.
[26]Calderone TL, Stevens RD, Oas TG. High-level misincorporation of lysine for arginine at AGA codons in a fusion protein expressed in Escherichia coli[J]. Journal of Molecular Biology, 1996, 262(4):407-412.
[27]Gurvich OL, Baranov PV, Gesteland RF, et al. Expression levels influence ribosomal frameshifting at the tandem rare arginine codons AGG_AGG and AGA_AGA in Escherichia coli[J]. Journal of Bacteriology, 2005, 187(12):4023-4032.
[28]McNulty DE, Claffee BA, Huddleston MJ, et al. Mistranslational errors associated with the rare arginine codon CGG in Escherichia coli[J]. Protein Expression and Purification, 2003, 27(2):365-374.
[29]Vyas VV, Esposito D, Sumpter TL, et al. Clinical manufacturing of recombinant human interleukin 15. I. Production cell line development and protein expression in E. coli with stop codon optimization[J]. Biotechnology Progress, 2012, 28(2):497-507.
[30]Whittaker MM, Whittaker JW. Expression and purification of recombinant Saccharomyces cerevisiae mitochondrial carrier protein YGR257Cp(Mtm1p)[J]. Protein Expression and Purification, 2014, 93:77-86.
[31]Li GW, Oh E, Weissman JS. The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria[J]. Nature, 2012, 484(7395):538-541.
[32]Deana A, Ehrlich R, Reiss C. Silent mutations in the Escherichia coli ompA leader peptide region strongly affect transcription and translation in vivo[J]. Nucleic Acids Research, 1998, 26(20):4778-4782.
[33]Duan JB, Wainwright MS, Comeron JM, et al. Synonymous mutations in the human dopamine receptor D2(DRD2)affect mRNA stability and synthesis of the receptor[J]. Human Molecular Genetics, 2003, 12(3):205-216.
[34]Pedersen M, Nissen S, Mitarai N, et al. The functional half-life of an mRNA depends on the ribosome spacing in an early coding region[J]. Journal of Molecular Biology, 2011, 407(1):35-44.
[35]Kudla G, Murray AW, Tollervey D, et al. Coding-Sequence determinants of gene expression in Escherichia coli[J]. Science, 2009, 324(5924):255-258.
[36]Makino S, Qu JN, Uemori K, et al. A silent mutation in the ftsH gene of Escherichia coli that affects FtsH protein production and colicin tolerance[J]. Molecular & General Genetics, 1997, 254(5):578-583.
[37]Hockenberry AJ, Sirer MI, Amaral LAN, et al. Quantifying position-dependent codon usage bias[J]. Molecular Biology and Evolution, 2014, 31(7):1880-1893.
[38]Bentele K, Saffert P, Rauscher R, et al. Efficient translation initiation dictates codon usage at gene start[J]. Molecular Systems Biology, 2013, 9:675.
[39] Goodman DB, Church GM, Kosuri S. Causes and effects of N-terminal codon bias in bacterial genes[J]. Science, 2013, 342(6157):475-479.
[40] Tang ZM, Salamanca-Pinzon SG, Wu ZL, et al. Human cytochrome P450 4F11:Heterologous expression in bacteria, purification, and characterization of catalytic function[J]. Archives of Biochemistry and Biophysics, 2010, 494(1):86-93.
[41] Mitarai N, Pedersen S. Control of ribosome traffic by position-dependent choice of synonymous codons[J]. Physical Biology, 2013, 10(5):056011.
[42]Chartier M, Gaudreault F, Najmanovich R. Large-scale analysis of conserved rare codon clusters suggests an involvement in co-translational molecular recognition events[J]. Bioinformatics, 2012, 28(11):1438-1445.
[43]Fluman N, Navon S, Bibi E, et al. mRNA-programmed translation pauses in the targeting of E. coli membrane proteins. [J]. Elife, 2014, 3. doi:10. 7554/eLife. 03440.