Abstract
Regulation of gene expression is fundamental for cellular function. Upon manipulation of the mechanism of gene expression in Escherichia coli, various bioproducts have been developed that are valuable industrially and medically in the last four decades. To efficiently produce bioproducts, numerous molecular tools are used for enhancing expression at the transcriptional and translational levels. Our recent discovery identified a new approach that enhances the gene expression in E. coli using the gene sequence of the eukaryote, Dictyostelium discoideum. In this review, we highlight the current molecular strategies used for high-level gene expression techniques commonly utilized in basic and applied microbiology.
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References
Arnold TE, Yu J, Belasco JG (1998) mRNA stabilization by the ompA 5′ untranslated region: two protective elements hinder distinct pathways for mRNA degradation. RNA 4:319–330
Aune TEV, Aachmann FL (2010) Methodologies to increase the transformation efficiencies and the range of bacteria that can be transformed. Appl Microbiol Biotechnol 85:1301–1313. https://doi.org/10.1007/s00253-009-2349-1
Belasco JG, Nilsson G, von Gabain A, Cohen SN (1986) The stability of E. coli gene transcripts is dependent on determinants localized to specific mRNA segments. Cell 46:245–251. https://doi.org/10.1016/0092-8674(86)90741-5
Benner SA, Sismour AM (2005) Synthetic biology. Nat Rev Genet 6:533–543. https://doi.org/10.1038/nrg1637
Boël G, Letso R, Neely H, Price WN, Wong K-H, Su M, Luff JD, Valecha M, Everett JK, Acton TB, Xiao R, Montelione GT, Aalberts DP, Hunt JF (2016) Codon influence on protein expression in E. coli correlates with mRNA levels. Nature 529:358–363. https://doi.org/10.1038/nature16509
Boni IV, Lsaeva DM, Musychenko ML, Tzareva NV (1991) Ribosome-messenger recognition: mRNA target sites for ribosomal protein S1. Nucleic Acids Res 19:155–162. https://doi.org/10.1093/nar/19.1.155
Burgess-Brown NA, Sharma S, Sobott F, Loenarz C, Oppermann U, Gileadi O (2008) Codon optimization can improve expression of human genes in Escherichia coli: a multi-gene study. Protein Expr Purif 59:94–102. https://doi.org/10.1016/j.pep.2008.01.008
Carrier TA, Keasling JD (1997a) Controlling messenger rna stability in bacteria: strategies for engineering gene expression. Biotechnol Prog 13:699–708. https://doi.org/10.1021/bp970095h
Carrier TA, Keasling JD (1997b) Engineering mRNA stability in E. coli by the addition of synthetic hairpins using a 5′ cassette system. Biotechnol Bioeng 55:577–580. https://doi.org/10.1002/(SICI)1097-0290(19970805)55:3<577::AID-BIT16>3.0.CO;2-D
Carrier TA, Keasling JD (1999) Library of synthetic 5′ secondary structures to manipulate mRNA stability in Escherichia coli. Biotechnol Prog 15:58–64. https://doi.org/10.1021/bp9801143
Chen LH, Emory SA, Bricker AL, Bouvet P, Belasco JG (1991) Structure and function of a bacterial mRNA stabilizer: analysis of the 5′ untranslated region of ompA mRNA. J Bacteriol 173:4578–4586. https://doi.org/10.1128/JB.173.15.4578-4586.1991
Chen H, Bjerknes M, Kumar R, Jay E (1994a) Determination of the optimal aligned spacing between the Shine–Dalgarno sequence and the translation initiation codon of Escherichia coli mRNAs. Nucleic Acids Res 22:4953–4957. https://doi.org/10.1093/nar/22.23.4953
Chen P, Ostrow BD, Tafuri SR, Chisholm RL (1994b) Targeted disruption of the Dictyostelium RMLC gene produces cells defective in cytokinesis and development. J Cell Biol 127:1933–1944. https://doi.org/10.1083/jcb.127.6.1933
Cohen SN, Chang ACY, Boyer HW, Helling RB (1973) Construction of biologically functional bacterial plasmids in vitro. Proc Natl Acad Sci U S A 70:3240–3244. https://doi.org/10.1073/pnas.70.11.3240
Coleman J, Inouye M, Nakamura K (1985) Mutations upstream of the ribosome-binding site affect translational efficiency. J Mol Biol 181:139–143. https://doi.org/10.1016/0022-2836(85)90332-8
de Boer HA, Comstock LJ, Vasser M (1983) The tac promoter: a functional hybrid derived from the trp and lac promoters. Proc Natl Acad Sci U S A 80:21–25. https://doi.org/10.1073/pnas.80.1.21
de Smit MH, van Duin J (1990) Control of prokaryotic translational initiation by mRNA secondary structure. Prog Nucleic Acid Res Mol Biol 38:1–35. https://doi.org/10.1016/s0079-6603(08)60707-2
de Smit MH, van Duin J (2003) Translational standby sites: how ribosomes may deal with the rapid folding kinetics of mRNA. J Mol Biol 331:737–743. https://doi.org/10.1016/S0022-2836(03)00809-X
Dong H, Nilsson L, Kurland CG (1995) Gratuitous overexpression of genes in Escherichia coli leads to growth inhibition and ribosome destruction. J Bacteriol 177:1497–1504. https://doi.org/10.1128/JB.177.6.1497-1504.1995
Eichinger I, Pachebat JA, Glöckner G, Rajandream MA, Sucgang R, Berriman M, Song J, Olsen R, Szafranski K, Xu Q, Tunggal B, Kummerfeld S, Madera M, Konfortov BA, Rivero F, Bankier AT, Lehmann R, Hamlin N, Davies R, Gaudet P, Fey P, Pilcher K, Chen G, Saunders D, Sodergren E, Davis P, Kerhornou A, Nie X, Hall N, Anjard C, Hemphill L, Bason N, Farbrother P, Desany B, Just E, Morio T, Rost R, Churcher C, Cooper J, Haydock S, Van Driessche N, Cronin A, Goodhead I, Muzny D, Mourier T, Pain A, Lu M, Harper D, Lindsay R, Hauser H, James K, Quiles M, Madan Babu M, Saito T, Buchrieser C, Wardroper A, Felder M, Thangavelu M, Johnson D, Knights A, Loulseged H, Mungall K, Oliver K, Price C, Quail MA, Urushihara H, Hernandez J, Rabbinowitsch E, Steffen D, Sanders M, Ma J, Kohara Y, Sharp S, Simmonds M, Spiegler S, Tivey A, Sugano S, White B, Walker D, Woodward J, Winckler T, Tanaka Y, Shaulsky G, Schleicher M, Weinstock G, Rosenthal A, Cox EC, Chisholm RL, Gibbs R, Loomis WF, Platzer M, Kay RR, Williams J, Dear PH, Noegel AA, Barrell B, Kuspa A (2005) The genome of the social amoeba Dictyostelium discoideum. Nature 435:43–57. https://doi.org/10.1038/nature03481
Eisenstein M (2019) Bring on the biosimilars. Nature 569:S2–S3. https://doi.org/10.1038/d41586-019-01401-5
Emory SA, Bouvet P, Belasco JG (1992) A 5′-terminal stem-loop structure can stabilize mRNA in Escherichia coli. Genes Dev 6:135–148. https://doi.org/10.1101/gad.6.1.135
Espah Borujeni A, Channarasappa AS, Salis HM (2014) Translation rate is controlled by coupled trade-offs between site accessibility, selective RNA unfolding and sliding at upstream standby sites. Nucleic Acids Res 42:2646–2659. https://doi.org/10.1093/nar/gkt1139
Fredens J, Wang K, de la Torre D, Funke LFH, Robertson WE, Christova Y, Chia T, Schmied WH, Dunkelmann DL, Beránek V, Uttamapinant C, Llamazares AG, Elliott TS, Chin JW (2019) Total synthesis of Escherichia coli with a recoded genome. Nature 569:514–518. https://doi.org/10.1038/s41586-019-1192-5
Goeddel DV, Kleid DG, Bolivar F (1979) Expression in Escherichia coli of chemically synthesized genes for human insulin. Proc Natl Acad Sci U S A 76:106–110. https://doi.org/10.1073/pnas.76.1.106
Goldstein J, Pollitt NS, Inouye M (1990) Major cold shock protein of Escherichia coli. Proc Natl Acad Sci U S A 87:283–287. https://doi.org/10.1073/pnas.87.1.283
Grylak-Mielnicka A, Bidnenko V, Bardowski J, Bidnenko E (2016) Transcription termination factor Rho: a hub linking diverse physiological processes in bacteria. Microbiology 162:433–447. https://doi.org/10.1099/mic.0.000244
Gusarov I, Nudler E (1999) The mechanism of intrinsic transcription termination. Mol Cell 3:495–504. https://doi.org/10.1016/S1097-2765(00)80477-3
Hannig G, Makrides SC (1998) Strategies for optimizing heterologous protein expression in Escherichia coli. Trends Biotechnol 16:54–60. https://doi.org/10.1016/S0167-7799(97)01155-4
Hayashi MN, Hayashi M (1985) Cloned DNA sequences that determine mRNA stability of bacteriophage ФX174 in vivo are functional. Nucleic Acids Res 13:5937–5948. https://doi.org/10.1093/nar/13.16.5937
Huang CJ, Lin H, Yang X (2012) Industrial production of recombinant therapeutics in Escherichia coli and its recent advancements. J Ind Microbiol Biotechnol 39:383–399. https://doi.org/10.1007/s10295-011-1082-9
Jiang W, Marraffini LA (2015) CRISPR-Cas: new tools for genetic manipulations from bacterial immunity systems. Annu Rev Microbiol 69:209–228. https://doi.org/10.1146/annurev-micro-091014-104441
Jiang W, Bikard D, Cox D, Zhang F, Marraffini LA (2013) RNA-guided editing of bacterial genomes using CRISPR-Cas systems. Nat Biotechnol 31:233–239. https://doi.org/10.1038/nbt.2508
Komarova AV, Tchufistova LS, Dreyfus M, Boni IV (2005) AU-rich sequences within 5′ untranslated leaders enhance translation and stabilize mRNA in Escherichia coli. J Bacteriol 187:1344–1349. https://doi.org/10.1128/JB.187.4.1344-1349.2005
Kondo T, Yumura S (2019) Translation enhancement by a Dictyostelium gene sequence in Escherichia coli. Appl Microbiol Biotechnol 103:3501–3510. https://doi.org/10.1007/s00253-019-09746-7
Kondo T, Yumura S (2020) An improved molecular tool for screening bacterial colonies using GFP expression enhanced by a Dictyostelium sequence. Biotechniques 68:91–95. https://doi.org/10.2144/btn-2019-0127
Koutmou KS, Schuller AP, Brunelle JL, Radhakrishnan A, Djuranovic S, Green R (2015) Ribosomes slide on lysine-encoding homopolymeric A stretches. Elife 4. https://doi.org/10.7554/eLife.05534
Kriner MA, Groisman EA (2017) RNA secondary structures regulate three steps of Rho-dependent transcription termination within a bacterial mRNA leader. Nucleic Acids Res 45:631–642. https://doi.org/10.1093/nar/gkw889
Lederberg J (1952) Cell genetics and hereditary symbiosis. Physiol Rev 32:403–430. https://doi.org/10.1152/physrev.1952.32.4.403
Li G-W, Oh E, Weissman JS (2012) The anti-Shine–Dalgarno sequence drives translational pausing and codon choice in bacteria. Nature 484:538–541. https://doi.org/10.1038/nature10965
Liu X, Gupta STPP, Bhimsaria D, Reed JL, Rodríguez-Martínez JA, Ansari AZ, Raman S (2019) De novo design of programmable inducible promoters. Nucleic Acids Res 47:10452–10463. https://doi.org/10.1093/nar/gkz772
Maertens B, Spriestersbach A, von Groll U, Roth U, Kubicek J, Gerrits M, Graf M, Liss M, Daubert D, Wagner R, Schäfer F (2010) Gene optimization mechanisms: a multi-gene study reveals a high success rate of full-length human proteins expressed in Escherichia coli. Protein Sci 19:1312–1326. https://doi.org/10.1002/pro.408
Makoff AJ, Oxer MD (1991) High level heterologous expression in E. coli using mutant forms of the lac promoter. Nucleic Acids Res 19:2417–2421. https://doi.org/10.1093/nar/19.9.2417
Makrides SC (1996) Strategies for achieving high-level expression of genes in Escherichia coli. Microbiol Rev 60:512–538
Mandel M, Higa A (1970) Calcium-dependent bacteriophage DNA infection. J Mol Biol 53:159–162 . https://doi.org/10.1016/0022-2836(70)90051-3
Marschall L, Sagmeister P, Herwig C (2017) Tunable recombinant protein expression in E. coli: promoter systems and genetic constraints. Appl Microbiol Biotechnol 101:501–512. https://doi.org/10.1007/s00253-016-8045-z
McCarthy JE, Schairer HU, Sebald W (1985) Translational initiation frequency of atp genes from Escherichia coli: identification of an intercistronic sequence that enhances translation. EMBO J 4:519–526. https://doi.org/10.1002/j.1460-2075.1985.tb03659.x
Meyer MM (2017) The role of mRNA structure in bacterial translational regulation. Wiley Interdiscip Rev RNA 8:e1370. https://doi.org/10.1002/wrna.1370
Min KT, Kim MH, Lee D-SS (1988) Search for the optimal sequence of the ribosome binding site by random oligonucleotide-directed mutagenesis. Nucleic Acids Res 16:5075–5088. https://doi.org/10.1093/nar/16.11.5075
Mitra P, Ghosh G, Hafeezunnisa M, Sen R (2017) Rho protein: roles and mechanisms. Annu Rev Microbiol 71:687–709. https://doi.org/10.1146/annurev-micro-030117-020432
Mohammad F, Woolstenhulme CJ, Green R, Buskirk AR (2016) Clarifying the translational pausing landscape in bacteria by ribosome profiling. Cell Rep 14:686–694. https://doi.org/10.1016/j.celrep.2015.12.073
Newbury SF, Smith NH, Robinson EC, Hiles ID, Higgins CF (1987) Stabilization of translationally active mRNA by prokaryotic REP sequences. Cell 48:297–310. https://doi.org/10.1016/0092-8674(87)90433-8
Nie Z, Luo H, Li J, Sun H, Xiao Y, Jia R, Liu T, Chang Y, Yu H, Shen Z (2020) High-throughput screening of T7 promoter mutants for soluble expression of cephalosporin C acylase in E. coli. Appl Biochem Biotechnol 190:293–304. https://doi.org/10.1007/s12010-019-03113-y
Olins PO, Devine CS, Rangwala SH, Kavka KS (1988) The T7 phage gene 10 leader RNA, a ribosome-binding site that dramatically enhances the expression of foreign genes in Escherichia coli. Gene 73:227–235. https://doi.org/10.1016/0378-1119(88)90329-0
Plotkin JB, Kudla G (2011) Synonymous but not the same: the causes and consequences of codon bias. Nat Rev Genet 12:32–42. https://doi.org/10.1038/nrg2899
Qu X, Lancaster L, Noller HF, Bustamante C, Tinoco I (2012) Ribosomal protein S1 unwinds double-stranded RNA in multiple steps. Proc Natl Acad Sci U S A 109:14458–14463. https://doi.org/10.1073/pnas.1208950109
Ringquist S, Shinedling S, Barrick D, Green L, Binkley J, Stormo GD, Gold L (1992) Translation initiation in Escherichia coli: sequences within the ribosome-binding site. Mol Microbiol 6:1219–1229. https://doi.org/10.1111/j.1365-2958.1992.tb01561.x
Roberts JW (1969) Termination factor for RNA synthesis. Nature 224:1168–1174. https://doi.org/10.1038/2241168a0
Roberts TM, Kacich R, Ptashne M (1979) A general method for maximizing the expression of a cloned gene. Proc Natl Acad Sci 76:760–764. https://doi.org/10.1073/pnas.76.2.760
Robinson M-PP, Ke N, Lobstein J, Peterson C, Szkodny A, Mansell TJ, Tuckey C, Riggs PD, Colussi PA, Noren CJ, Taron CH, DeLisa MP, Berkmen M (2015) Efficient expression of full-length antibodies in the cytoplasm of engineered bacteria. Nat Commun 6:8072. https://doi.org/10.1038/ncomms9072
Rosenfeld L (2002) Insulin: discovery and controversy. Clin Chem 48:2270–2288
Salis HM, Mirsky EA, Voigt CA (2009) Automated design of synthetic ribosome binding sites to control protein expression. Nat Biotechnol 27:946–950. https://doi.org/10.1038/nbt.1568
Scherer GFE, Walkinshaw MD, Arnott S, Morré DJ (1980) The ribosome binding sites recognized by E. coli ribosomes have regions with signal character in both the leader and protein coding segments. Nucleic Acids Res 8:3895–3908. https://doi.org/10.1093/nar/8.17.3895
Shepard HM, Yelverton E, Goeddel DV (1982) Increased synthesis in E. coli of fibroblast and leukocyte interferons through alterations in ribosome binding sites. DNA 1:125–131. https://doi.org/10.1089/dna.1.1982.1.125
Shine J, Dalgarno L (1974) The 3′ terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites. Proc Natl Acad Sci U S A 71:1342–1346. https://doi.org/10.1073/pnas.71.4.1342
Souza L, Boone T, Gabrilove J, Lai P, Zsebo K, Murdock D, Chazin V, Bruszewski J, Lu H, Chen K, Barendt J, Platzer E, Moore MAS, Mertelsmann R, Welte K (1986) Recombinant human granulocyte colony-stimulating factor: effects on normal and leukemic myeloid cells. Science (80) 232:61–65. https://doi.org/10.1126/science.232.4746.61
Spadiut O, Capone S, Krainer F, Glieder A, Herwig C (2014) Microbials for the production of monoclonal antibodies and antibody fragments. Trends Biotechnol 32:54–60. https://doi.org/10.1016/j.tibtech.2013.10.002
Stanssens P, Remaut E, Fiers W (1985) Alterations upstream from the Shine-Dalgarno region and their effect on bacterial gene expression. Gene 36:211–223. https://doi.org/10.1016/0378-1119(85)90176-3
Steitz JA, Jakes K (1975) How ribosomes select initiator regions in mRNA: base pair formation between the 3′ terminus of 16S rRNA and the mRNA during initiation of protein synthesis in Escherichia coli. Proc Natl Acad Sci 72:4734–4738. https://doi.org/10.1073/pnas.72.12.4734
Studier FW, Moffatt BA (1986) Use of bacteriophage T7 RNA polymerase to direct selective high-level expression of cloned genes. J Mol Biol 189:113–130. https://doi.org/10.1016/0022-2836(86)90385-2
Studier FW, Rosenberg AH, Dunn JJ, Dubendorff JW (1990) Use of T7 RNA polymerase to direct expression of cloned genes. Methods Enzymol 185:60–89. https://doi.org/10.1016/0076-6879(90)85008-c
Takahashi S, Furusawa H, Ueda T, Okahata Y (2013) Translation enhancer improves the ribosome liberation from translation initiation. J Am Chem Soc 135:13096–13106. https://doi.org/10.1021/ja405967h
Taketo A (1988) DNA transfection of Escherichia coli by electroporation. Biochim Biophys Acta 949:318–324. https://doi.org/10.1016/0167-4781(88)90158-3
Tats A, Tenson T, Remm M (2008) Preferred and avoided codon pairs in three domains of life. BMC Genomics 9:463. https://doi.org/10.1186/1471-2164-9-463
Taylor A, Brown D, Kadam S, Maus M, Kohlbrenner W, Weigl D, Turon M, Katz L (1992) High-level expression and purification of mature HIV-1 protease in Escherichia coli under control of the araBAD promoter. Appl Microbiol Biotechnol 37:205–210. https://doi.org/10.1007/BF00178172
Tian J, Yan Y, Yue Q, Liu X, Chu X, Wu N, Fan Y (2017) Predicting synonymous codon usage and optimizing the heterologous gene for expression in E. coli. Sci Rep 7:9926. https://doi.org/10.1038/s41598-017-10546-0
Vimberg V, Tats A, Remm M, Tenson T (2007) Translation initiation region sequence preferences in Escherichia coli. BMC Mol Biol 8:1–13. https://doi.org/10.1186/1471-2199-8-100
Walsh G (2018) Biopharmaceutical benchmarks 2018. Nat Biotechnol 36:1136–1145. https://doi.org/10.1038/nbt.4305
Yusupova G, Jenner L, Rees B, Moras D, Yusupov M (2006) Structural basis for messenger RNA movement on the ribosome. Nature 444:391–394. https://doi.org/10.1038/nature05281
Zhang S, Zubay G, Goldman E (1991) Low-usage codons in Escherichia coli, yeast, fruit fly and primates. Gene 105:61–72. https://doi.org/10.1016/0378-1119(91)90514-C
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This article was supported by the Japan Society for the Promotion of Science KAKENHI Grant Number 16J08310 and 19K15809 to TK.
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Kondo, T., Yumura, S. Strategies for enhancing gene expression in Escherichia coli. Appl Microbiol Biotechnol 104, 3825–3834 (2020). https://doi.org/10.1007/s00253-020-10430-4
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DOI: https://doi.org/10.1007/s00253-020-10430-4