Skip to main content

Cell-Free Display Techniques for Protein Evolution

  • Chapter
  • First Online:
Cell-free Macromolecular Synthesis

Part of the book series: Advances in Biochemical Engineering/Biotechnology ((ABE,volume 185))

Abstract

Cell-free protein synthesis (CFPS) with flexibility and controllability can provide a powerful platform for high-throughput screening of biomolecules, especially in the evolution of peptides or proteins. In this chapter, the emerging strategies for enhancing the protein expression level using different source strains, energy systems, and template designs in constructing CFPS systems are summarized and discussed in detail. In addition, we provide an overview of the ribosome display, mRNA display, cDNA display, and CIS display in vitro display technologies, which can couple genotype and phenotype by forming fusion complexes. Moreover, we point out the trend that improving the protein yields of CFPS itself can offer more favorable conditions for maintaining library diversity and display efficiency. It is hoped that the novel CFPS system can accelerate the development of protein evolution in biotechnological and medical applications.

Graphical Abstract

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 229.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD 299.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Galeffi P, Lombardi A, Pietraforte I, Novelli F, Di Donato M, Sperandei M, Tornambe A, Fraio-li R, Martayan A, Natali PG, Benevolo M, Mottolese M, Ylera F, Cantale C, Giacomini P (2006) Functional expression of a single-chain antibody to ErbB-2 in plants and cell-free systems. J Transl Med 4:39. https://doi.org/10.1186/1479-5876-4-3914

    Article  PubMed  PubMed Central  Google Scholar 

  2. Jiang X, Ookubo Y, Fujii I, Nakano H, Yamane T (2002) Expression of Fab fragment of catalytic antibody 6D9 in an Escherichia coli in vitro coupled transcription/translation system. FEBS Lett 514(2–3):290–294. https://doi.org/10.1016/s0014-5793(02)02383-915

    Article  CAS  PubMed  Google Scholar 

  3. Dondapati SK, Kreir M, Quast RB, Wustenhagen DA, Bruggemann A, Fertig N, Kubick S (2014) Membrane assembly of the functional KcsA potassium channel in a vesicle-based eukaryotic cell-free translation system. Biosens Bioelectron 59:174–183. https://doi.org/10.1016/j.bios.2014.03.00418

    Article  CAS  PubMed  Google Scholar 

  4. Nozawa A, Nanamiya H, Miyata T, Linka N, Endo Y, Weber AP, Tozawa Y (2007) A cell-free translation and proteoliposome reconstitution system for functional analysis of plant solute transporters. Plant Cell Physiol 48(12):1815–1820. https://doi.org/10.1093/pcp/pcm15017

    Article  CAS  PubMed  Google Scholar 

  5. Sachse R, Dondapati SK, Fenz SF, Schmidt T, Kubick S (2014) Membrane protein synthesis in cell-free systems: from bio-mimetic systems to bio-membranes. FEBS Lett 588(17):2774–2781. https://doi.org/10.1016/j.febslet.2014.06.00716

    Article  CAS  PubMed  Google Scholar 

  6. Goering AW, Li J, McClure RA, Thomson RJ, Jewett MC, Kelleher NL (2017) In vitro reconstruction of nonribosomal peptide biosynthesis directly from DNA using cell-free protein synthesis. ACS Synth Biol 6(1):39–44. https://doi.org/10.1021/acssynbio.6b0016020

    Article  CAS  PubMed  Google Scholar 

  7. Mikami S, Kobayashi T, Masutani M, Yokoyama S, Imataka H (2008) A human cell-derived in vitro coupled transcription/translation system optimized for production of recombinant proteins. Protein Expr Purif 62(2):190–198. https://doi.org/10.1016/j.pep.2008.09.00219

    Article  CAS  PubMed  Google Scholar 

  8. Jaroentomeechai T, Stark JC, Natarajan A, Glasscock CJ, Yates LE, Hsu KJ, Mrksich M, Jew-ett MC, DeLisa MP (2018) Single-pot glycoprotein biosynthesis using a cell-free transcription-translation system enriched with glycosylation machinery. Nat Commun 9(1):2686. https://doi.org/10.1038/s41467-018-05110-x21

    Article  PubMed  PubMed Central  Google Scholar 

  9. Shimizu Y, Inoue A, Tomari Y, Suzuki T, Yokogawa T, Nishikawa K, Ueda T (2001) Cell-free translation reconstituted with purified components. Nat Biotechnol 19(8):751–755. https://doi.org/10.1038/908026

    Article  CAS  PubMed  Google Scholar 

  10. Shimizu Y, Kanamori T, Ueda T (2005) Protein synthesis by pure translation systems. Methods 36(3):299–304. https://doi.org/10.1016/j.ymeth.2005.04.00622

    Article  CAS  PubMed  Google Scholar 

  11. Wang HH, Huang PY, Xu G, Haas W, Marblestone A, Li J, Gygi SP, Forster AC, Jewett MC, Church GM (2012) Multiplexed in vivo His-tagging of enzyme pathways for in vitro single-pot multienzyme catalysis. ACS Synth Biol 1(2):43–52. https://doi.org/10.1021/sb300002926

    Article  PubMed  PubMed Central  Google Scholar 

  12. Villarreal F, Contreras-Llano LE, Chavez M, Ding YF, Fan JZ, Pan TR, Tan CM (2018) Syn-thetic microbial consortia enable rapid assembly of pure translation machinery. Nat Chem Biol 14(1):29–35. https://doi.org/10.1038/Nchembio.251425

    Article  CAS  PubMed  Google Scholar 

  13. Shepherd TR, Du L, Liljeruhm J, Samudyata WJ, Sjodin MOD, Wetterhall M, Yomo T, Forster AC (2017) De novo design and synthesis of a 30-cistron translation-factor module. Nucleic Acids Res 45(18):10895–10905. https://doi.org/10.1093/nar/gkx75324

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Lavickova B, Maerkl SJ (2019) A Simple, robust, and low-cost method to produce the PUR-E cell-free system. ACS Synth Biol 8(2):455–462. https://doi.org/10.1021/acssynbio.8b0042723

    Article  CAS  PubMed  Google Scholar 

  15. Smith GP (1985) Filamentous fusion phage: novel expression vectors that display cloned antigens on the virion surface. Science 228(4705):1315–1317. https://doi.org/10.1126/science.4001944232

    Article  CAS  PubMed  Google Scholar 

  16. Marks JD, Hoogenboom HR, Griffiths AD, Winter G (1992) Molecular evolution of proteins on filamentous phage. Mimicking the strategy of the immune system. J Biol Chem 267(23):16007–16010. https://doi.org/10.1016/s0021-9258(18)41952-7230

    Article  CAS  PubMed  Google Scholar 

  17. Boder ET, Midelfort KS, Wittrup KD (2000) Directed evolution of antibody fragments with monovalent femtomolar antigen-binding affinity. Proc Natl Acad Sci U S A 97(20):10701–10705. https://doi.org/10.1073/pnas.170297297233

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Contreras-Llano LE, Tan C (2018) High-throughput screening of biomolecules using cell-free gene expression systems. Synth Biol (Oxf) 3(1):ysy012. https://doi.org/10.1093/synbio/ysy012177

    Article  CAS  PubMed  Google Scholar 

  19. Prevel C, Kurzawa L, Van TN, Morris MC (2014) Fluorescent biosensors for drug discovery n-ew tools for old targets – screening for inhibitors of cyclin-dependent kinases. Eur J Med Chem 88:74–88. https://doi.org/10.1016/j.ejmech.2014.10.003245

    Article  CAS  PubMed  Google Scholar 

  20. Doyle SK, Pop MS, Evans HL, Koehler AN (2016) Advances in discovering small molecules to probe protein function in a systems context. Curr Opin Chem Biol 30:28–36. https://doi.org/10.1016/j.cbpa.2015.10.032246

    Article  CAS  PubMed  Google Scholar 

  21. Longwell CK, Labanieh L, Cochran JR (2017) High-throughput screening technologies for enzyme engineering. Curr Opin Biotechnol 48:196–202. https://doi.org/10.1016/j.copbio.2017.05.012247

    Article  CAS  PubMed  Google Scholar 

  22. Perez JG, Stark JC, Jewett MC (2016) Cell-free synthetic biology: engineering beyond the cell. Cold Spring Harb Perspect Biol 8(12):a023853. https://doi.org/10.1101/cshperspect.a02385333

    Article  PubMed  PubMed Central  Google Scholar 

  23. Nirenberg MW, Matthaei JH (1961) The dependence of cell-free protein synthesis in E. coli upon naturally occurring or synthetic polyribonucleotides. Proc Natl Acad Sci U S A 47(10):1588–1602. https://doi.org/10.1073/pnas.47.10.158846

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Kwon YC, Jewett MC (2015) High-throughput preparation methods of crude extract for robust cell-free protein synthesis. Sci Rep 58:663. https://doi.org/10.1038/srep0866332

    Article  Google Scholar 

  25. Caschera F, Noireaux V (2014) Synthesis of 2.3 mg/ml of protein with an all Escherichia coli cell-free transcription-translation system. Biochimie 99:162–168. https://doi.org/10.1016/j.biochi.2013.11.02530

    Article  CAS  PubMed  Google Scholar 

  26. Guzman-Chavez F, Arce A, Adhikari A, Vadhin S, Pedroza-Garcia JA, Gandini C, Ajioka JW, Molloy J, Sanchez-Nieto S, Varner JD, Federici F, Haseloff J (2022) Constructing cell-free expression systems for low-cost access. ACS Synth Biol 11(3):1114–1128. https://doi.org/10.1021/acssynbio.1c0034231

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Zawada JF, Yin G, Steiner AR, Yang J, Naresh A, Roy SM, Gold DS, Heinsohn HG, Murray CJ (2011) Microscale to manufacturing scale-up of cell-free cytokine production – a new appro-ach for shortening protein production development timelines. Biotechnol Bioeng 108(7):1570–1578. https://doi.org/10.1002/bit.2310335

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Nakashima N, Tamura T (2004) Cell-free protein synthesis using cell extract of pseudomonas fluorescens and CspA promoter. Biochem Biophys Res Commun 319(2):671–676. https://doi.org/10.1016/j.bbrc.2004.05.03448

    Article  CAS  PubMed  Google Scholar 

  29. Wang H, Li J, Jewett MC (2018) Development of a pseudomonas putida cell-free protein synthesis platform for rapid screening of gene regulatory elements. Synth Biol (Oxf) 3(1):ysy003. https://doi.org/10.1093/synbio/ysy00349

    Article  CAS  PubMed  Google Scholar 

  30. Yang C, Yang M, Zhao W, Ding Y, Wang Y, Li J (2022) Establishing a Klebsiella pneumoniae-based cell-free protein synthesis system. Molecules 27(15):4684. https://doi.org/10.3390/molecules2715468450

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Li J, Wang H, Kwon YC, Jewett MC (2017) Establishing a high yielding streptomyces-based cell-free protein synthesis system. Biotechnol Bioeng 114(6):1343–1353. https://doi.org/10.1002/bit.2625337

    Article  CAS  PubMed  Google Scholar 

  32. Li J, Wang H, Jewett MC (2018) Expanding the palette of Streptomyces-based cell-free protein synthesis systems with enhanced yields. Biochem Eng J 130:29–33. https://doi.org/10.1016/j.bej.2017.11.01336

    Article  CAS  Google Scholar 

  33. Xu H, Liu WQ, Li J (2020) Translation related factors improve the productivity of a streptomyces-based cell-free protein synthesis system. ACS Synth Biol 9(5):1221–1224. https://doi.org/10.1021/acssynbio.0c0014038

    Article  CAS  PubMed  Google Scholar 

  34. Xu H, Yang C, Tian X, Chen Y, Liu WQ, Li J (2022) Regulatory part engineering for high-yield protein synthesis in an all-streptomyces-based cell-free expression system. ACS Synth Biol 11(2):570–578. https://doi.org/10.1021/acssynbio.1c0058739

    Article  CAS  PubMed  Google Scholar 

  35. Kelwick R, Webb AJ, MacDonald JT, Freemont PS (2016) Development of a Bacillus subtilis cell-free transcription-translation system for prototyping regulatory elements. Metab Eng 38:370–381. https://doi.org/10.1016/j.ymben.2016.09.00881

    Article  CAS  PubMed  Google Scholar 

  36. Suresh G, Cabezudo I, Pulicharla R, Cuprys A, Rouissi T, Brar SK (2020) Biodegradation of aflatoxin B1 with cell-free extracts of Trametes versicolor and Bacillus subtilis. Res Vet Sci 133:85–91. https://doi.org/10.1016/j.rvsc.2020.09.00983

    Article  CAS  PubMed  Google Scholar 

  37. Moore SJ, MacDonald JT, Wienecke S, Ishwarbhai A, Tsipa A, Aw R, Kylilis N, Bell DJ, Mc-Clymont DW, Jensen K, Polizzi KM, Biedendieck R, Freemont PS (2018) Rapid acquisition and model-based analysis of cell-free transcription-translation reactions from nonmodel bacteria. Proc Natl Acad Sci U S A 115(19):E4340–E4349. https://doi.org/10.1073/pnas.171580611585

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Uzawa T, Yamagishi A, Oshima T (2002) Polypeptide synthesis directed by DNA as a messeng-er in cell-free polypeptide synthesis by extreme thermophile, Thermus thermophilus HB27 and -Sulfolobus tokodaii strain 7. J Biochem 131(6):849–853. https://doi.org/10.1093/oxfordjournals.jbchem.a00317441

    Article  CAS  PubMed  Google Scholar 

  39. Endoh T, Kanai T, Sato YT, Liu DV, Yoshikawa K, Atomi H, Imanaka T (2006) Cell-free protein synthesis at high temperatures using the lysate of a hyperthermophile. J Biotechnol 126(2):186–195. https://doi.org/10.1016/j.jbiotec.2006.04.01042

    Article  CAS  PubMed  Google Scholar 

  40. Lo Gullo G, Mattossovich R, Perugino G, La Teana A, Londei P, Benelli D (2019) Optimization of an in vitro transcription/translation system based on Sulfolobus solfataricus cell lysate. Archaea 2019:9848253. https://doi.org/10.1155/2019/984825343

    Article  PubMed  PubMed Central  Google Scholar 

  41. Eagon RG (1962) Pseudomonas natriegens, a marine bacterium with a generation time of less than 10 minutes. J Bacteriol 83(4):736–737. https://doi.org/10.1128/jb.83.4.736-737.196277

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Aiyar SE, Gaal T, Gourse RL (2002) rRNA promoter activity in the fast-growing bacterium vibrio natriegens. J Bacteriol 184(5):1349–1358. https://doi.org/10.1128/JB.184.5.1349-1358.200278

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Des Soye BJ, Davidson SR, Weinstock MT, Gibson DG, Jewett MC (2018) Establishing a high-yielding cell-free protein synthesis platform derived from vibrio natriegens. ACS Synth Biol 7(9):2245–2255. https://doi.org/10.1021/acssynbio.8b0025256

    Article  CAS  PubMed  Google Scholar 

  44. Wiegand DJ, Lee HH, Ostrov N, Church GM (2018) Establishing a cell-free vibrio natriegens expression system. ACS Synth Biol 7(10):2475–2479. https://doi.org/10.1021/acssynbio.8b0022258

    Article  CAS  PubMed  Google Scholar 

  45. Gan R, Jewett MC (2014) A combined cell-free transcription-translation system from Saccharomyces cerevisiae for rapid and robust protein synthe. Biotechnol J 9(5):641–651. https://doi.org/10.1002/biot.201300545134

    Article  CAS  PubMed  Google Scholar 

  46. Hodgman CE, Jewett MC (2013) Optimized extract preparation methods and reaction conditions for improved yeast cell-free protein synthesis. Biotechnol Bioeng 110(10):2643–2654. https://doi.org/10.1002/bit.24942135

    Article  CAS  PubMed  Google Scholar 

  47. Schoborg JA, Hodgman CE, Anderson MJ, Jewett MC (2014) Substrate replenishment and byproduct removal improve yeast cell-free protein synthesis. Biotechnol J 9(5):630–640. https://doi.org/10.1002/biot.201300383137

    Article  CAS  PubMed  Google Scholar 

  48. Brodiazhenko T, Johansson MJO, Takada H, Nissan T, Hauryliuk V, Murina V (2018) Elimination of ribosome inactivating factors improves the efficiency of Bacillus subtilis and Saccharomyces cerevisiae cell-free translation systems. Front Microbiol 9:3041. https://doi.org/10.3389/fmicb.2018.03041133

    Article  PubMed  PubMed Central  Google Scholar 

  49. Hodgman CE, Jewett MC (2014) Characterizing IGR IRES-mediated translation initiation for use in yeast cell-free protein synthesis. N Biotechnol 31(5):499–505. https://doi.org/10.1016/j.nbt.2014.07.001140

    Article  CAS  PubMed  Google Scholar 

  50. Anderson MJ, Stark JC, Hodgman CE, Jewett MC (2015) Energizing eukaryotic cell-free protein synthesis with glucose metabolism. FEBS Lett 589(15):1723–1727. https://doi.org/10.1016/j.febslet.2015.05.045141

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Rasor BJ, Yi X, Brown H, Alper HS, Jewett MC (2021) An integrated in vivo/in vitro frame-work to enhance cell-free biosynthesis with metabolically rewired yeast extracts. Nat Commun 12(1):5139. https://doi.org/10.1038/s41467-021-25233-y136

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Endo Y, Sawasaki T (2006) Cell-free expression systems for eukaryotic protein production. Curr Opin Biotechnol 17(4):373–380. https://doi.org/10.1016/j.copbio.2006.06.00964

    Article  CAS  PubMed  Google Scholar 

  53. Fogeron ML, Lecoq L, Cole L, Harbers M, Bockmann A (2021) Easy synthesis of complex bi-omolecular assemblies: wheat germ cell-free protein expression in structural biology. Front Mol Biosci 8:639587. https://doi.org/10.3389/fmolb.2021.63958765

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Harbers M (2014) Wheat germ systems for cell-free protein expression. FEBS Lett 588(17):2762–2773. https://doi.org/10.1016/j.febslet.2014.05.06168

    Article  CAS  PubMed  Google Scholar 

  55. Goshima N, Kawamura Y, Fukumoto A, Miura A, Honma R, Satoh R, Wakamatsu A, Yamamoto J, Kimura K, Nishikawa T, Andoh T, Iida Y, Ishikawa K, Ito E, Kagawa N, Kaminaga C, Kanehori K, Kawakami B, Kenmochi K, Kimura R, Kobayashi M, Kuroita T, Kuwayama H, Maruyama Y, Matsuo K, Minami K, Mitsubori M, Mori M, Morishita R, Murase A, Nishikawa A, Nishikawa S, Okamoto T, Sakagami N, Sakamoto Y, Sasaki Y, Seki T, Sono S, Sugiyama A, Sumiya T, Takayama T, Takayama Y, Takeda H, Togashi T, Yahata K, Yamada H, Yanagisawa Y, Endo Y, Imamoto F, Kisu Y, Tanaka S, Isogai T, Imai J, Watanabe S, Nomura N (2008) Human protein factory for converting the transcriptome into an in vitro-expressed proteome. Nat Methods 5(12):1011–1017. https://doi.org/10.1038/nmeth.127367

    Article  CAS  PubMed  Google Scholar 

  56. Kanoi BN, Nagaoka H, Morita M, Tsuboi T, Takashima E (2021) Leveraging the wheat germ cell-free protein synthesis system to accelerate malaria vaccine development. Parasitol Int 80:102224. https://doi.org/10.1016/j.parint.2020.10222469

    Article  CAS  PubMed  Google Scholar 

  57. Buntru M, Vogel S, Spiegel H, Schillberg S (2014) Tobacco BY-2 cell-free lysate: an alternative and highly-productive plant-based in vitro translation system. BMC Biotechnol 14:37. https://doi.org/10.1186/1472-6750-14-3773

    Article  PubMed  PubMed Central  Google Scholar 

  58. Buntru M, Vogel S, Stoff K, Spiegel H, Schillberg S (2015) A versatile coupled cell-free transcription-translation system based on tobacco BY-2 cell lysates. Biotechnol Bioeng 112(5):867–878. https://doi.org/10.1002/bit.2550274

    Article  CAS  PubMed  Google Scholar 

  59. Suzuki K, Inoue H, Matsuoka S, Tero R, Hirano-Iwata A, Tozawa Y (2020) Establishment of a cell-free translation system from rice callus extracts. Biosci Biotechnol Biochem 84(10):2028–2036. https://doi.org/10.1080/09168451.2020.177902462

    Article  CAS  PubMed  Google Scholar 

  60. Murota K, Hagiwara-Komoda Y, Komoda K, Onouchi H, Ishikawa M, Naito S (2011) Arabidopsis cell-free extract, ACE, a new in vitro translation system derived from Arabidopsis callus cultures. Plant Cell Physiol 52(8):1443–1453. https://doi.org/10.1093/pcp/pcr08080

    Article  CAS  PubMed  Google Scholar 

  61. Cordoba-Canero D, Roldan-Arjona T, Ariza RR (2012) Using Arabidopsis cell extracts to monitor repair of DNA base damage in vitro. Methods Mol Biol 920:263–277. https://doi.org/10.1007/978-1-61779-998-3_18103

    Article  CAS  PubMed  Google Scholar 

  62. Liu K, Hu J (2018) Host-regulated hepatitis B virus capsid assembly in a mammalian cell-free system. Bio Protoc 8(8):e2813. https://doi.org/10.21769/BioProtoc.2813100

    Article  PubMed  PubMed Central  Google Scholar 

  63. Panthu B, Ohlmann T, Perrier J, Schlattner U, Jalinot P, Elena-Herrmann B, Rautureau GJP (2018) Cell-free protein synthesis enhancement from real-time NMR metabolite kinetics: red-irecting energy fluxes in hybrid RRL systems. ACS Synth Biol 7(1):218–226. https://doi.org/10.1021/acssynbio.7b00280101

    Article  CAS  PubMed  Google Scholar 

  64. Anastasina M, Terenin I, Butcher SJ, Kainov DE (2014) A technique to increase protein yield in a rabbit reticulocyte lysate translation system. Biotechniques 56(1):36–39. https://doi.org/10.2144/00011412599

    Article  CAS  PubMed  Google Scholar 

  65. Brodel AK, Sonnabend A, Kubick S (2014) Cell-free protein expression based on extracts from CHO cells. Biotechnol Bioeng 111(1):25–36. https://doi.org/10.1002/bit.25013101

    Article  PubMed  Google Scholar 

  66. Ramm F, Jack L, Kaser D, Schlosshauer JL, Zemella A, Kubick S (2022) Cell-free systems enable the production of AB5 toxins for diagnostic applications. Toxins (Basel) 14(4):233. https://doi.org/10.3390/toxins1404023389

    Article  CAS  PubMed  Google Scholar 

  67. Thoring L, Dondapati SK, Stech M, Wustenhagen DA, Kubick S (2017) High-yield production of “difficult-to-express” proteins in a continuous exchange cell-free system based on CHO cell lysates. Sci Rep 7(1):11710. https://doi.org/10.1038/s41598-017-12188-8103

    Article  PubMed  PubMed Central  Google Scholar 

  68. Yadavalli R, Sam-Yellowe T (2015) HeLa based cell free expression systems for expression of plasmodium Rhoptry proteins. J Vis Exp (100):e52772. https://doi.org/10.3791/52772269

  69. Wustenhagen DA, Lukas P, Muller C, Aubele SA, Hildebrandt JP, Kubick S (2020) Cell-free synthesis of the hirudin variant 1 of the blood-sucking leech Hirudo medicinalis. Sci Rep 10(1):19818. https://doi.org/10.1038/s41598-020-76715-w272

    Article  PubMed  PubMed Central  Google Scholar 

  70. Burgenson D, Gurramkonda C, Pilli M, Ge X, Andar A, Kostov Y, Tolosa L, Rao G (2018) Rap-id recombinant protein expression in cell-free extracts from human blood. Sci Rep 8(1):9569. https://doi.org/10.1038/s41598-018-27846-8270

    Article  PubMed  PubMed Central  Google Scholar 

  71. Mikami S, Masutani M, Sonenberg N, Yokoyama S, Imataka H (2006) An efficient mammalian cell-free translation system supplemented with translation factors. Protein Expr Purif 46(2):348–357. https://doi.org/10.1016/j.pep.2005.09.021105

    Article  CAS  PubMed  Google Scholar 

  72. Brodel AK, Sonnabend A, Roberts LO, Stech M, Wustenhagen DA, Kubick S (2013) IRES-mediated translation of membrane proteins and glycoproteins in eukaryotic cell-free systems. PloS One 8(12):e82234. https://doi.org/10.1371/journal.pone.0082234138

    Article  PubMed  PubMed Central  Google Scholar 

  73. Merk H, Rues RB, Gless C, Beyer K, Dong F, Dotsch V, Gerrits M, Bernhard F (2015) Biosynthesis of membrane dependent proteins in insect cell lysates: identification of limiting parameters for folding and processing. Biol Chem 396(9–10):1097–1107. https://doi.org/10.1515/hsz-2015-010588

    Article  CAS  PubMed  Google Scholar 

  74. Suzuki T, Ezure T, Ando E, Nishimura O, Utsumi T, Tsunasawa S (2010) Preparation of ubiquitin-conjugated proteins using an insect cell-free protein synthesis system. J Biotechnol 145(1):73–78. https://doi.org/10.1016/j.jbiotec.2009.10.00991

    Article  CAS  PubMed  Google Scholar 

  75. Quast RB, Claussnitzer I, Merk H, Kubick S, Gerrits M (2014) Synthesis and site-directed fluorescence labeling of azido proteins using eukaryotic cell-free orthogonal translation systems. Anal Biochem 451:4–9. https://doi.org/10.1016/j.ab.2014.01.013139

    Article  CAS  PubMed  Google Scholar 

  76. Stech M, Hust M, Schulze C, Dubel S, Kubick S (2014) Cell-free eukaryotic systems for the production, engineering, and modification of scFv antibody fragments. Eng Life Sci 14(4):387–398. https://doi.org/10.1002/elsc.20140003690

    Article  CAS  PubMed  Google Scholar 

  77. Zemella A, Thoring L, Hoffmeister C, Kubick S (2015) Cell-free protein synthesis: pros and cons of prokaryotic and eukaryotic systems. Chembiochem 16(17):2420–2431. https://doi.org/10.1002/cbic.20150034093

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. Mureev S, Kovtun O, Nguyen UT, Alexandrov K (2009) Species-independent translational leaders facilitate cell-free expression. Nat Biotechnol 27(8):747–752. https://doi.org/10.1038/nbt.155698

    Article  CAS  PubMed  Google Scholar 

  79. Cui Z, Wu Y, Mureev S, Alexandrov K (2018) Oligonucleotide-mediated tRNA sequestration enables one-pot sense codon reassignment in vitro. Nucleic Acids Res 46(12):6387–6400. https://doi.org/10.1093/nar/gky36595

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  80. Kovtun O, Mureev S, Jung W, Kubala MH, Johnston W, Alexandrov K (2011) Leishmania cell-free protein expression system. Methods 55(1):58–64. https://doi.org/10.1016/j.ymeth.2011.06.00697

    Article  CAS  PubMed  Google Scholar 

  81. Johnston WA, Moradi SV, Alexandrov K (2019) Adaption of the Leishmania cell-free expression system to high-throughput analysis of protein interactions. Methods Mol Biol 2025:403–421. https://doi.org/10.1007/978-1-4939-9624-7_1996

    Article  CAS  PubMed  Google Scholar 

  82. Bhide M, Natarajan S, Hresko S, Aguilar C, Bencurova E (2014) Rapid in vitro protein synthesis pipeline: a promising tool for cost-effective protein array design. Mol Biosyst 10(6):1236–1245. https://doi.org/10.1039/c4mb00003j94

    Article  CAS  PubMed  Google Scholar 

  83. Kigawa T, Yabuki T, Yoshida Y, Tsutsui M, Ito Y, Shibata T, Yokoyama S (1999) Cell-free pro-duction and stable-isotope labeling of milligram quantities of proteins. FEBS Lett 442(1):15–19. https://doi.org/10.1016/S0014-5793(98)01620-2144

    Article  CAS  PubMed  Google Scholar 

  84. Kim DM, Swartz JR (2001) Regeneration of adenosine triphosphate from glycolytic intermediates for cell-free protein synthesis. Biotechnol Bioeng 74(4):309-316. 129

    Article  Google Scholar 

  85. Jewett MC, Swartz JR (2004) Mimicking the Escherichia coli cytoplasmic environment activates long-lived and efficient cell-free protein synthesis. Biotechnol Bioeng 86(1):19–26. https://doi.org/10.1002/bit.20026126

    Article  CAS  PubMed  Google Scholar 

  86. Cai Q, Hanson JA, Steiner AR, Tran C, Masikat MR, Chen R, Zawada JF, Sato AK, Hallam TJ, Yin G (2015) A simplified and robust protocol for immunoglobulin expression in Escherichia coli cell-free protein synthesis systems. Biotechnol Prog 31(3):823–831. https://doi.org/10.1002/btpr.2082140

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  87. Schoborg JA, Hershewe JM, Stark JC, Kightlinger W, Kath JE, Jaroentomeechai T, Natarajan A, DeLisa MP, Jewett MC (2018) A cell-free platform for rapid synthesis and testing of active oligosaccharyltransferases. Biotechnol Bioeng 115(3):739–750. https://doi.org/10.1002/bit.26502141

    Article  CAS  PubMed  Google Scholar 

  88. Sitaraman K, Esposito D, Klarmann G, Le Grice SF, Hartley JL, Chatterjee DK (2004) A novel cell-free protein synthesis system. J Biotechnol 110(3):257–263. https://doi.org/10.1016/j.jbiotec.2004.02.014131

    Article  CAS  PubMed  Google Scholar 

  89. Kim TW, Keum JW, Oh IS, Choi CY, Kim HC, Kim DM (2007) An economical and highly productive cell-free protein synthesis system utilizing fructose-1,6-bisphosphate as an energy source. J Biotechnol 130(4):389–393. https://doi.org/10.1016/j.jbiotec.2007.05.002142

    Article  CAS  PubMed  Google Scholar 

  90. Kim H-C, Kim T-W, Kim D-M (2011) Prolonged production of proteins in a cell-free protein synthesis system using polymeric carbohydrates as an energy source. Process Biochem 46(6):1366–1369. https://doi.org/10.1016/j.procbio.2011.03.008139

    Article  CAS  Google Scholar 

  91. Jewett MC, Calhoun KA, Voloshin A, Wuu JJ, Swartz JR (2008) An integrated cell-free meta-bolic platform for protein production and synthetic biology. Mol Syst Biol 4:220. https://doi.org/10.1038/msb.2008.57145

    Article  PubMed  PubMed Central  Google Scholar 

  92. Akanuma G, Kobayashi A, Suzuki S, Kawamura F, Shiwa Y, Watanabe S, Yoshikawa H, Hana-i R, Ishizuka M (2014) Defect in the formation of 70S ribosomes caused by lack of ribosomal protein L34 can be suppressed by magnesium. J Bacteriol 196(22):3820–3830. https://doi.org/10.1128/Jb.01896-14147

    Article  PubMed  PubMed Central  Google Scholar 

  93. Garamella J, Marshall R, Rustad M, Noireaux V (2016) The all E. coli TX-TL toolbox 2.0: a platform for cell-free synthetic biology. ACS Synth Biol 5(4):344–355. https://doi.org/10.1021/acssynbio.5b00296148

    Article  CAS  PubMed  Google Scholar 

  94. Michel-Reydellet N, Woodrow K, Swartz J (2005) Increasing PCR fragment stability and protein yields in a cell-free system with genetically modified Escherichia coli extracts. J Mol Microbiol Biotechnol 9(1):26–34. https://doi.org/10.1159/000088143160

    Article  CAS  PubMed  Google Scholar 

  95. Seki E, Matsuda N, Kigawa T (2009) Multiple inhibitory factor removal from an Escherichia co-li cell extract improves cell-free protein synthesis. J Biosci Bioeng 108(1):30–35. https://doi.org/10.1016/j.jbiosc.2009.02.011161

    Article  CAS  PubMed  Google Scholar 

  96. Batista AC, Levrier A, Soudier P, Voyvodic PL, Achmedov T, Reif-Trauttmansdorff T, DeVis-ch A, Cohen-Gonsaud M, Faulon JL, Beisel CL, Bonnet J, Kushwaha M (2022) Differentially optimized cell-free buffer enables robust expression from unprotected linear DNA in exonuclease-deficient extracts. ACS Synth Biol 11(2):732–746. https://doi.org/10.1021/acssynbio.1c00448159

    Article  CAS  PubMed  Google Scholar 

  97. Marshall R, Maxwell CS, Collins SP, Beisel CL, Noireaux V (2017) Short DNA containing c-hi sites enhances DNA stability and gene expression in E. coli cell-free transcription-translation systems. Biotechnol Bioeng 114(9):2137–2141. https://doi.org/10.1002/bit.26333152

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  98. Spies M, Amitani I, Baskin RJ, Kowalczykowski SC (2007) RecBCD enzyme switches lead motor subunits in response to chi recognition. Cell 131(4):694–705. https://doi.org/10.1016/j.cell.2007.09.023168

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  99. Amundsen SK, Spicer T, Karabulut AC, Londono LM, Eberhart C, Fernandez Vega V, Banni-ster TD, Hodder P, Smith GR (2012) Small-molecule inhibitors of bacterial AddAB and RecBCD helicase-nuclease DNA repair enzymes. ACS Chem Biol 7(5):879–891. https://doi.org/10.1021/cb300018x169

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  100. Yim SS, Johns NI, Noireaux V, Wang HH (2020) Protecting linear DNA templates in cell- free expression systems from diverse bacteria. ACS Synth Biol 9(10):2851–2855. https://doi.org/10.1021/acssynbio.0c00277157

    Article  CAS  PubMed  Google Scholar 

  101. Zhu B, Gan R, Cabezas MD, Kojima T, Nicol R, Jewett MC, Nakano H (2020) Increasing cell-free gene expression yields from linear templates in Escherichia coli and vibrio natriegens extracts by using DNA-binding proteins. Biotechnol Bioeng 117(12):3849–3857. https://doi.org/10.1002/bit.27538158

    Article  CAS  PubMed  Google Scholar 

  102. Sun ZZ, Yeung E, Hayes CA, Noireaux V, Murray RM (2014) Linear DNA for rapid prototyping of synthetic biological circuits in an Escherichia coli based TX-TL cell-free system. ACS Synth Biol 3(6):387–397. https://doi.org/10.1021/sb400131a163

    Article  CAS  PubMed  Google Scholar 

  103. Hong SH, Ntai I, Haimovich AD, Kelleher NL, Isaacs FJ, Jewett MC (2014) Cell-free protein synthesis from a release factor 1 deficient Escherichia coli activates efficient and multiple site- specific nonstandard amino acid incorporation. ACS Synth Biol 3(6):398–409. https://doi.org/10.1021/sb400140t162

    Article  CAS  PubMed  Google Scholar 

  104. Wu PS, Ozawa K, Lim SP, Vasudevan SG, Dixon NE, Otting G (2007) Cell-free transcription/translation from PCR-amplified DNA for high-throughput NMR studies. Angew Chem Int Ed Engl 46(18):3356–3358. https://doi.org/10.1002/anie.200605237170

    Article  CAS  PubMed  Google Scholar 

  105. Ahn JH, Chu HS, Kim TW, Oh IS, Choi CY, Hahn GH, Park CG, Kim DM (2005) Cell-free synthesis of recombinant proteins from PCR-amplified genes at a comparable productivity to that of plasmid-based reactions. Biochem Biophys Res Commun 338(3):1346–1352. https://doi.org/10.1016/j.bbrc.2005.10.094165

    Article  CAS  PubMed  Google Scholar 

  106. Chen X, Lu Y (2021) In silico design of linear DNA for robust cell-free gene expression. Front Bioeng Biotechnol 9:670341. https://doi.org/10.3389/fbioe.2021.670341151

    Article  PubMed  PubMed Central  Google Scholar 

  107. Mattheakis LC, Bhatt RR, Dower WJ (1994) An in vitro polysome display system for identifying ligands from very large peptide libraries. Proc Natl Acad Sci U S A 91(19):9022–9026. https://doi.org/10.1073/pnas.91.19.9022215

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  108. Pluckthun A, Schaffitzel C, Hanes J, Jermutus L (2001) In vitro selection and evolution of proteins. Adv Protein Chem 55:367–403. https://doi.org/10.1016/s0065-3233(01)55009-3

    Article  Google Scholar 

  109. Zahnd C, Amstutz P, Pluckthun A (2007) Ribosome display: selecting and evolving proteins in vitro that specifically bind to a target. Nat Methods 4(3):269–279. https://doi.org/10.1038/nmeth1003183

    Article  CAS  PubMed  Google Scholar 

  110. Ahangarzadeh S, Bandehpour M, Kazemi B (2017) Selection of single-chain variable fragments specific for mycobacterium tuberculosis ESAT-6 antigen using ribosome display. Iran J Basic Med Sci 20(3):327–333. https://doi.org/10.22038/ijbms.2017.8363222

    Article  PubMed  PubMed Central  Google Scholar 

  111. Gan R, Jewett MC (2016) Evolution of translation initiation sequences using in vitro yeast ribosome display. Biotechnol Bioeng 113(8):1777–1786. https://doi.org/10.1002/bit.25933223

    Article  CAS  PubMed  Google Scholar 

  112. He M, Taussig MJ (1997) Antibody-ribosome-mRNA (ARM) complexes as efficient selection particles for in vitro display and evolution of antibody combining sites. Nucleic Acids Res 25(24):5132–5134. https://doi.org/10.1093/nar/25.24.5132221

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  113. Villemagne D, Jackson R, Douthwaite JA (2006) Highly efficient ribosome display selection by use of purified components for in vitro translation. J Immunol Methods 313(1–2):140–148. https://doi.org/10.1016/j.jim.2006.04.001184

    Article  CAS  PubMed  Google Scholar 

  114. Ohashi H, Kanamori T, Osada E, Akbar BK, Ueda T (2012) Peptide screening using PURE ribosome display. Methods Mol Biol 805:251–259. https://doi.org/10.1007/978-1-61779-379-0_14217

    Article  CAS  PubMed  Google Scholar 

  115. Ueda T, Kanamori T, Ohashi H (2010) Ribosome display with the PURE technology. Methods Mol Biol 607:219–225. https://doi.org/10.1007/978-1-60327-331-2_18218

    Article  CAS  PubMed  Google Scholar 

  116. Kanamori T, Fujino Y, Ueda T (2014) PURE ribosome display and its application in antibody technology. Biochim Biophys Acta 1844(11):1925–1932. https://doi.org/10.1016/j.bbapap.2014.04.007219

    Article  CAS  PubMed  Google Scholar 

  117. Luginbuhl B, Kanyo Z, Jones RM, Fletterick RJ, Prusiner SB, Cohen FE, Williamson RA, B-urton DR, Pluckthun A (2006) Directed evolution of an anti-prion protein scFv fragment to an affinity of 1 pM and its structural interpretation. J Mol Biol 363(1):75–97. https://doi.org/10.1016/j.jmb.2006.07.027225

    Article  PubMed  Google Scholar 

  118. Dreier B, Pluckthun A (2012) Rapid selection of high-affinity binders using ribosome display. Methods Mol Biol 805:261–286. https://doi.org/10.1007/978-1-61779-379-0_15224

    Article  CAS  PubMed  Google Scholar 

  119. Kunamneni A, Ogaugwu C, Bradfute S, Durvasula R (2020) Ribosome display technology: applications in disease diagnosis and control. Antibodies (Basel) 9(3):28. https://doi.org/10.3390/antib9030028185

    Article  CAS  PubMed  Google Scholar 

  120. Stefan N, Martin-Killias P, Wyss-Stoeckle S, Honegger A, Zangemeister-Wittke U, Pluckthun A (2011) DARPins recognizing the tumor-associated antigen EpCAM selected by phage and ribosome display and engineered for multivalency. J Mol Biol 413(4):826–843. https://doi.org/10.1016/j.jmb.2011.09.016226

    Article  CAS  PubMed  Google Scholar 

  121. Hammerling MJ, Fritz BR, Yoesep DJ, Kim DS, Carlson ED, Jewett MC (2020) In vitro ribosome synthesis and evolution through ribosome display. Nat Commun 11(1):1108. https://doi.org/10.1038/s41467-020-14705-2174

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  122. Roberts RW, Szostak JW (1997) RNA-peptide fusions for the in vitro selection of peptides and proteins. Proc Natl Acad Sci U S A 94(23):12297–12302. https://doi.org/10.1073/pnas.94.23.12297228

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  123. Wang R, Cotten SW, Liu R (2012) mRNA display using covalent coupling of mRNA to translated proteins. Methods Mol Biol 805:87–100. https://doi.org/10.1007/978-1-61779-379-0_6192

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  124. Kurz M, Gu K, Lohse PA (2000) Psoralen photo-crosslinked mRNA–puromycin conjugates: a novel template for the rapid and facile preparation of mRNA–protein fusions. Nucleic Acids Res 28(18):e83–e83. https://doi.org/10.1093/nar/28.18.e83237

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  125. Moore MJ, Sharp PA (1992) Site-specific modification of pre-mRNA: the 2′-hydroxyl groups at the splice sites. Science 256(5059):992–997. https://doi.org/10.1126/science.1589782236

    Article  CAS  PubMed  Google Scholar 

  126. Miyamoto-Sato E, Takashima H, Fuse S, Sue K, Ishizaka M, Tateyama S, Horisawa K, Sawasaki T, Endo Y, Yanagawa H (2003) Highly stable and efficient mRNA templates for mRNA-protein fusions and C-terminally labeled proteins. Nucleic Acids Res 31(15):e78. https://doi.org/10.1093/nar/gng078234

    Article  PubMed  PubMed Central  Google Scholar 

  127. Seelig B (2011) mRNA display for the selection and evolution of enzymes from in vitro-translated protein libraries. Nat Protoc 6(4):540–552. https://doi.org/10.1038/nprot.2011.312235

    Article  CAS  PubMed  Google Scholar 

  128. Nagumo Y, Fujiwara K, Horisawa K, Yanagawa H, Doi N (2016) PURE mRNA display for in vitro selection of single-chain antibodies. J Biochem 159(5):519–526. https://doi.org/10.1093/jb/mvv131198

    Article  CAS  PubMed  Google Scholar 

  129. Takahashi K, Sunohara M, Terai T, Kumachi S, Nemoto N (2017) Enhanced mRNA-protein fusion efficiency of a single-domain antibody by selection of mRNA display with additional rand-om sequences in the terminal translated regions. Biophys Physicobiol 14:23–28. https://doi.org/10.2142/biophysico.14.0_23199

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  130. Bacon K, Bowen J, Reese H, Rao BM, Menegatti S (2020) Use of target-displaying magnetized yeast in screening mRNA-display peptide libraries to identify ligands. ACS Comb Sci 22(12):738–744. https://doi.org/10.1021/acscombsci.0c00171201

    Article  CAS  PubMed  Google Scholar 

  131. Ishizawa T, Kawakami T, Reid PC, Murakami H (2013) TRAP display: a high-speed selection method for the generation of functional polypeptides. J Am Chem Soc 135(14):5433–5440. https://doi.org/10.1021/ja312579u238

    Article  CAS  PubMed  Google Scholar 

  132. Muranaka N, Hohsaka T, Sisido M (2006) Four-base codon mediated mRNA display to construct peptide libraries that contain multiple nonnatural amino acids. Nucleic Acids Res 34(1):e7. https://doi.org/10.1093/nar/gnj003202

    Article  PubMed  PubMed Central  Google Scholar 

  133. Tabata N, Sakuma Y, Honda Y, Doi N, Takashima H, Miyamoto-Sato E, Yanagawa H (2009) Rapid antibody selection by mRNA display on a microfluidic chip. Nucleic Acids Res 37(8):e64-e64. https://doi.org/10.1093/nar/gkp184241

    Article  Google Scholar 

  134. Olson CA, Nie J, Diep J, Al-Shyoukh I, Takahashi TT, Al-Mawsawi LQ, Bolin JM, Elwell AL, Swanson S, Stewart R, Thomson JA, Soh HT, Roberts RW, Sun R (2012) Single-round, multiplexed antibody mimetic design through mRNA display. Angew Chem Int Ed 51(50):12449–12453. https://doi.org/10.1002/anie.201207005240

    Article  CAS  Google Scholar 

  135. Kamide (2009) Isolation of novel cell-penetrating peptides from a random peptide library using in vitro virus and their modifications. Int J Mol Med 25(01):41–51. https://doi.org/10.3892/ijmm_00000311243

    Article  Google Scholar 

  136. Fukuda I, Kojoh K, Tabata N, Doi N, Takashima H, Miyamoto-Sato E, Yanagawa H (2006) In vitro evolution of single-chain antibodies using mRNA display. Nucleic Acids Res 34(19):e127. https://doi.org/10.1093/nar/gkl618242

    Article  PubMed  PubMed Central  Google Scholar 

  137. Duan H, Kachko A, Zhong L, Struble E, Pandey S, Yan H, Harman C, Virata-Theimer ML, De-ng L, Zhao Z, Major M, Feinstone S, Zhang P (2012) Amino acid residue-specific neutralization and nonneutralization of hepatitis C virus by monoclonal antibodies to the E2 protein. J Virol 86(23):12686–12694. https://doi.org/10.1128/JVI.00994-12244

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  138. Yamaguchi J, Naimuddin M, Biyani M, Sasaki T, Machida M, Kubo T, Funatsu T, Husimi Y, Nemoto N (2009) cDNA display: a novel screening method for functional disulfide-rich peptides by solid-phase synthesis and stabilization of mRNA-protein fusions. Nucleic Acids Res 37(16):e108. https://doi.org/10.1093/nar/gkp514203

    Article  PubMed  PubMed Central  Google Scholar 

  139. Mochizuki Y, Nemoto N (2012) Evolution of disulfide-rich peptide aptamers using cDNA display. Methods Mol Biol 805:237–250. https://doi.org/10.1007/978-1-61779-379-0_13211

    Article  CAS  PubMed  Google Scholar 

  140. Mochizuki Y, Biyani M, Tsuji-Ueno S, Suzuki M, Nishigaki K, Husimi Y, Nemoto N (2011) One-pot preparation of mRNA/cDNA display by a novel and versatile puromycin-linker DNA. ACS Comb Sci 13(5):478–485. https://doi.org/10.1021/co2000295214

    Article  CAS  PubMed  Google Scholar 

  141. Ueno S, Kimura S, Ichiki T, Nemoto N (2012) Improvement of a puromycin-linker to extend the selection target varieties in cDNA display method. J Biotechnol 162(2–3):299–302. https://doi.org/10.1016/j.jbiotec.2012.09.003204

    Article  CAS  PubMed  Google Scholar 

  142. Mochizuki Y, Suzuki T, Fujimoto K, Nemoto N (2015) A versatile puromycin-linker using cnvK for high-throughput in vitro selection by cDNA display. J Biotechnol 212:174–180. https://doi.org/10.1016/j.jbiotec.2015.08.020206

    Article  CAS  PubMed  Google Scholar 

  143. Terai T, Koike T, Nemoto N (2020) Photocrosslinking of cDNA display molecules with their target proteins as a new strategy for peptide selection. Molecules 25(6):1472. https://doi.org/10.3390/molecules25061472209

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  144. Hino M, Kataoka M, Kajimoto K, Yamamoto T, Kido J, Shinohara Y, Baba Y (2008) Efficiency of cell-free protein synthesis based on a crude cell extract from Escherichia coli, wheat germ, and rabbit reticulocytes. J Biotechnol 133(2):183–189. https://doi.org/10.1016/j.jbiotec.2007.08.008250

    Article  CAS  PubMed  Google Scholar 

  145. Anzai H, Terai T, Jayathilake C, Suzuki T, Nemoto N (2019) A novel immuno-PCR method using cDNA display. Anal Biochem 578:1–6. https://doi.org/10.1016/j.ab.2019.04.017252

    Article  CAS  PubMed  Google Scholar 

  146. Jayathilake C, Kumachi S, Arai H, Motohashi M, Terai T, Murakami A, Nemoto N (2020) In vitro selection of anti-gliadin single-domain antibodies from a naive library for cDNA-display mediated immuno-PCR. Anal Biochem 589:113490. https://doi.org/10.1016/j.ab.2019.113490253

    Article  CAS  PubMed  Google Scholar 

  147. Reyes SG, Kuruma Y, Fujimi M, Yamazaki M, Eto S, Nishikawa S, Tamaki S, Kobayashi A, Mizuuchi R, Rothschild L, Ditzler M, Fujishima K (2021) PURE mRNA display and cDNA dis-play provide rapid detection of core epitope motif via high-throughput sequencing. Biotechnol Bioeng 118(4):1736–1749. https://doi.org/10.1002/bit.27696251

    Article  CAS  PubMed  Google Scholar 

  148. Naimuddin M, Kobayashi S, Tsutsui C, Machida M, Nemoto N, Sakai T, Kubo T (2011) Direct-ed evolution of a three-finger neurotoxin by using cDNA display yields antagonists as well as agonists of interleukin-6 receptor signaling. Mol Brain 4(1):2. https://doi.org/10.1186/1756-6606-4-2249

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  149. Nemoto N, Kumachi S, Arai H (2018) In vitro selection of single-domain antibody (VHH) using cDNA display. Methods Mol Biol 1827:269–285. https://doi.org/10.1007/978-1-4939-8648-4_14210

    Article  CAS  PubMed  Google Scholar 

  150. Kondo T, Eguchi M, Kito S, Fujino T, Hayashi G, Murakami H (2021) cDNA TRAP display for rapid and stable in vitro selection of antibody-like proteins. Chem Commun (Camb) 57(19):2416–2419. https://doi.org/10.1039/d0cc07541h212

    Article  CAS  PubMed  Google Scholar 

  151. Odegrip R, Coomber D, Eldridge B, Hederer R, Kuhlman PA, Ullman C, FitzGerald K, McGre-gor D (2004) CIS display: in vitro selection of peptides from libraries of protein-DNA complexes. Proc Natl Acad Sci U S A 101(9):2806–2810. https://doi.org/10.1073/pnas.0400219101262

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  152. Patel S, Mathonet P, Jaulent AM, Ullman CG (2013) Selection of a high-affinity WW domain against the extracellular region of VEGF receptor isoform-2 from a combinatorial library using CIS display. Protein Eng Des Sel 26(4):307–315. https://doi.org/10.1093/protein/gzt003256

    Article  CAS  PubMed  Google Scholar 

  153. Mathonet P, Ioannou A, Betley J, Ullman C (2011) CIS display, a DNA-based in vitro selection technology for therapeutic peptides. Chim Oggi-Chem Today 29(2):10–12. 267. https://www.researchgate.net/publication/233734623

    CAS  Google Scholar 

  154. Reiersen H, Lobersli I, Loset GA, Hvattum E, Simonsen B, Stacy JE, McGregor D, Fitzgerald K, Welschof M, Brekke OH, Marvik OJ (2005) Covalent antibody display – an in vitro antibody-DNA library selection system. Nucleic Acids Res 33(1):e10. https://doi.org/10.1093/nar/gni010259

    Article  PubMed  PubMed Central  Google Scholar 

  155. Galan A, Comor L, Horvatic A, Kules J, Guillemin N, Mrljak V, Bhide M (2016) Library-based display technologies: where do we stand? Mol Biosyst 12(8):2342–2358. https://doi.org/10.1039/c6mb00219f258

    Article  CAS  PubMed  Google Scholar 

  156. Norouzi M, Panfilov S, Pardee K (2021) High-efficiency protection of linear DNA in cell-free extracts from Escherichia coli and vibrio natriegens. ACS Synth Biol 10(7):1615–1624. https://doi.org/10.1021/acssynbio.1c0011057

    Article  CAS  PubMed  Google Scholar 

  157. Fan J, Villarreal F, Weyers B, Ding Y, Tseng KH, Li J, Li B, Tan C, Pan T (2017) Multi-dimensional studies of synthetic genetic promoters enabled by microfluidic impact printing. Lab Chip 17(13):2198–2207. https://doi.org/10.1039/c7lc00382j266

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  158. Syu GD, Dunn J, Zhu H (2020) Developments and applications of functional protein microarrays. Mol Cell Proteomics 19(6):916–927. https://doi.org/10.1074/mcp.R120.001936265

    Article  PubMed  PubMed Central  Google Scholar 

  159. Blanco C, Verbanic S, Seelig B, Chen IA (2020) High throughput sequencing of in vitro select-ions of mRNA-displayed peptides: data analysis and applications. Phys Chem Chem Phys 22(12):6492–6506. https://doi.org/10.1039/c9cp05912a193

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgments

This work was supported by the National Key R&D Program of China (Grant No. 2019YFA0904103).

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Hao Qi .

Editor information

Editors and Affiliations

Ethics declarations

Author Contributions

JJL and YHY contributed equally to this work. JJL designed the framework and drafted the original manuscript. YHY collected the related literature and drew the figs. HQ conceived the presented idea and supervised the writing of the article. All authors contributed to the article and approved the submitted version.

Rights and permissions

Reprints and permissions

Copyright information

© 2023 The Author(s), under exclusive license to Springer Nature Switzerland AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Li, J., Yang, Y., Li, J., Li, P., Qi, H. (2023). Cell-Free Display Techniques for Protein Evolution. In: Lu, Y., Jewett, M.C. (eds) Cell-free Macromolecular Synthesis. Advances in Biochemical Engineering/Biotechnology, vol 185. Springer, Cham. https://doi.org/10.1007/10_2023_227

Download citation

Publish with us

Policies and ethics