Abstract
Ribosome display is a powerful engineering research tool for the high-throughput selection of peptides or proteins, which results in the generation of high-performance binders against nearly any antigen of interest. As a cell-free display system, ribosome display has been well developed with many outstanding achievements for over 20 years. Compared with other related display techniques, ribosome display shows unique advantages and development prospects. This tool has been successfully exploited for the selection of functional and specific binders in vitro. This review provides a comprehensive survey of the applications of ribosome display in screening or evolving functional proteins as well as in diagnostics and therapeutics. Previous papers on ribosome display failed to comprehensively review evolutionary strategies for proteins. In the present paper, we review all existing evolutionary strategies that have been combined with ribosome display. We also discuss shortcomings, improvement strategies, and research tendency.
Similar content being viewed by others
Abbreviations
- E. coli :
-
Escherichia coli
- scFv:
-
Single-chain variable fragment
- SPR:
-
Surface plasmon resonance
- RFs:
-
Release factors
- RRFs:
-
Ribosome recycling factors
- Cκ:
-
Constant region of Igκ chain
- CH:
-
Heavy chain constant domain
- PCR:
-
Polymerase chain reaction
- RT-PCR:
-
Reverse transcription-polymerase chain reaction
- VHH:
-
Variable region of a heavy chain antibody
- PM:
-
Parsimonious mutagenesis
- RAGE:
-
Receptor for advanced glycation end products
- DARPins:
-
Designed ankyrin repeat proteins
- StEP:
-
Staggered extension process
- IAA:
-
Indoleacetic acid
- PrP:
-
Prion protein
- BSA:
-
Bovine serum albumin
- T-NHL:
-
T-cell non-Hodgkin lymphoma
- DTT:
-
Dithiothreitol
- HCV:
-
Hepatitis C virus
- HCVcc:
-
HCV cell culture
- PURE:
-
Protein synthesis using recombinant elements
- ECD:
-
Extracellular domain
- Her2:
-
Human epidermal growth factor receptor 2
- K D :
-
Equilibrium dissociation constants
- VH:
-
Heavy chain variable domain
- K:
-
The complete constant region of the mouse κ light chain
- pM:
-
Picomolar
References
Farajnia, S., Ahmadzadeh, V., Tanomand, A., Veisi, K., Khosroshahi, S. A., & Rahbarnia, L. (2014). Development trends for generation of single-chain antibody fragments. Immunopharmacology and Immunotoxicology, 36, 297–308.
McCafferty, J., & Schofield, D. (2015). Identification of optimal protein binders through the use of large genetically encoded display libraries. Current Opinion in Chemical Biology, 26, 16–24.
Low, N. M., Holliger, P. H., & Winter, G. (1996). Mimicking somatic hypermutation: affinity maturation of antibodies displayed on bacteriophage using a bacterial mutator strain. Journal of Molecular Biology, 260, 359–368.
Li, M., Fan, X., Liu, J., Hu, Y., & Huang, H. (2015). Selection by phage display of nanobodies directed against hypoxia inducible factor-1alpha (HIF-1alpha). Biotechnology and Applied Biochemistry, 62, 738–745.
Mattheakis, L. C., Bhatt, R. R., & Dower, W. J. (1994). An in vitro polysome display system for identifying ligands from very large peptide libraries. Proceedings of the National Academy of Sciences of the United States of America, 91, 9022–9026.
Douthwaite, J. A., & Jackson, R. H. (2012) Ribosome display and related technologies. New York: Humana Press.
Shang, G., Feng, D., Lu, F., Zhang, H., Cang, H., Gao, W., & Bi, R. (2014). Purification, crystallization and preliminary crystallographic analysis of a ribosome-recycling factor from Thermoanaerobacter tengcongensis (TteRRF). Acta Crystallographica F, 70, 588–591.
He, M., & Taussig, M. J. (2002) Ribosome display: Cell-free protein display technology. Briefings in Functional Genomics & Proteomics, 1, 204–212.
Hanes, J., & Plückthun, A. (1997). In vitro Selection and Evolution of Functional Proteins by Using Ribosome Display. Proceedings of the National Academy of Sciences of the United States of America, 94, 4937–4942.
Zhao, X.-L., Chen, W.-Q., Yang, Z.-H., Li, J.-M., Zhang, S.-J., & Tian, L.-F. (2009). Selection and affinity maturation of human antibodies against rabies virus from a scFv gene library using ribosome display. Journal of Biotechnology, 144, 253–258.
Bencurova, E., Pulzova, L., Flachbartova, Z., & Bhide, M. (2015). A rapid and simple pipeline for synthesis of mRNA-ribosome-VHH complexes used in single-domain antibody ribosome display. Molecular Biosystems, 11, 1515–1524.
Pacheco, S., Canton, E., Zuniga-Navarrete, F., Pecorari, F., Bravo, A., & Soberon, M. (2015). Improvement and efficient display of Bacillus thuringiensis toxins on M13 phages and ribosomes. AMB Express., 5, 73.
Manandhar, Y., Wang, W., Inoue, J., Hayashi, N., Uzawa, T., Ito, Y., Aigaki, T., & Ito, Y. (2017). Interactions of in vitro selected fluorogenic peptide aptamers with calmodulin. Biotechnology Letter, 39, 375–382.
Hanes, J., Jermutus, L., Schaffitzel, C., & Plückthun, A. (1999). Comparison of Escherichia coli and rabbit reticulocyte ribosome display systems. FEBS Letters, 450, 105–110.
Zahnd, C., Amstutz, P., & Pluckthün, A. (2007). Ribosome display: Selecting and evolving proteins in vitro that specifically bind to a target. Nature Methods, 4, 269–279.
Pardon, E., Laeremans, T., Triest, S., Rasmussen, S. G. F., Wohlkönig, A., Ruf, A., Muyldermans, S., Hol, W. G. J., Kobilka, B. K., & Steyaert, J. (2014). A general protocol for the generation of nanobodies for structural biology. Nature Protocols, 9, 674–693.
Zadravec, P., Mareckova, L., Petrokova, H., Hodnik, V., Perisic Nanut, M., Anderluh, G., Strukelj, B., Maly, P., & Berlec, A. (2016). Development of recombinant lactococcus lactis displaying albumin-binding domain variants against shiga toxin 1 B subunit. PLoS ONE, 11, e0162625.
Zhao, X. L., Tian, L. F., Zhang, S. J., Li, J. M., Feng, H., Wang, L. M., Wang, S., Wang, J., Wang, T., & Chen, W. Q. (2016). Novel human three-domain antibody fragments against sTNF alpha as well as tmTNF alpha with high affinity generated by the combination of ribosome display and E. coli expression system. Scandinavian Journal of Immunology, 83, 267–278.
Pan, Y., Mao, W., Liu, X., Xu, C., He, Z., Wang, W., & Yan, H. (2012). Selection of single chain variable fragments specific for the human-inducible costimulator using ribosome display. Applied Biochemistry and Biotechnology, 168, 967–979.
Ahangarzadeh, S., Bandehpour, M., & Kazemi, B. (2017). Selection of single-chain variable fragments specific for Mycobacterium tuberculosis ESAT-6 antigen using ribosome display. Iranian Journal of Basic Medical Sciences, 20, 327–333.
He, M., & Taussig, M. J. (1997). Antibody-ribosome-mRNA (ARM) complexes as efficient selection particles for in vitro display and evolution of antibody combining sites. Nucleic Acids Research, 25, 5132–5134.
Gan, R., & Jewett, M. C. (2016). Evolution of translation initiation sequences using in vitro yeast ribosome display. Biotechnology and Bioengineering, 113, 1777–1786.
Douthwaite, J. A., Groves, M. A., Dufner, P., & Jermutus, L. (2006). An improved method for an efficient and easily accessible eukaryotic ribosome display technology. Protein Engineering Design & Selection Peds, 19, 85–90.
Veggiani, G., Ossolengo, G., Aliprandi, M., Cavallaro, U., & De, M. A. (2011) Single-domain antibodies that compete with the natural ligand fibroblast growth factor block the internalization of the fibroblast growth factor receptor 1. Biochemical & Biophysical Research Communications, 408, 692–696.
Murray, C. J., & Baliga, R. (2013). Cell-free translation of peptides and proteins: from high throughput screening to clinical production. Current Opinion in Chemical Biology, 17, 420–426.
Blondel, M., Soubigou, F., Evrard, J., Nguyen, P. H., Hasin, N., Chedin, S., Gillet, R., Contesse, M. A., Friocourt, G., Stahl, G., Jones, G. W., & Voisset, C. (2016). Protein folding activity of the ribosome is involved in yeast prion propagation. Science Report, 6, 32117.
Forster, A. C., Cornish, V. W., & Blacklow, S. C. (2004). Pure translation display. Analytical Biochemistry, 333, 358–364.
Chong, S. (2014) Overview of cell-free protein synthesis: historic landmarks, commercial systems, and expanding applications. Current Protocols in Molecular Biology, 108, 16.30.1–16.30.11.
Cong, C., Yu, X., He, Y. Z., Dai, Y. J., Zhang, Y. X., Wang, M. R., & He, M. Y. (2016). Cell-free ribosome display and selection of antibodies on arrayed antigens. Proteomics, 16, 1291–1296.
Lipovsek, D., & Plückthun, A. (2004). In-vitro protein evolution by ribosome display and mRNA display. Journal of Immunological Methods, 290, 51–67.
Kim, J. M., Shin, H. J., Kim, K., & Lee, M. S. (2007). A pseudoknot improves selection efficiency in ribosome display. Molecular Biotechnology, 36, 32–37.
Yau, K. Y., Dubuc, G., Li, S., Hirama, T., Mackenzie, C. R., Jermutus, L., Hall, J. C., & Tanha, J. (2005). Affinity maturation of a V(H)H by mutational hotspot randomization. Journal of Immunological Methods, 297, 213–224.
Finlay, W. J., Cunningham, O., Lambert, M. A., Darmanin-Sheehan, A., Liu, X., Fennell, B. J., Mahon, C. M., Cummins, E., Wade, J. M., & O’Sullivan, C. M. (2009). Affinity maturation of a humanized rat antibody for Anti-RAGE therapy: Comprehensive mutagenesis reveals a high level of mutational plasticity both inside and outside the complementarity-determining regions. Journal of Molecular Biology, 388, 541–558.
Zahnd, C., Wyler, E., Schwenk, J. M., Steiner, D., Lawrence, M. C., McKern, N. M., Pecorari, F., Ward, C. W., Joos, T. O., & Pluckthun, A. (2007). A designed ankyrin repeat protein evolved to picomolar affinity to Her2. Journal of Molecular Biology, 369, 1015–1028.
Po, K., Chan, E., & Chen, S. (2017) Functional characterization of CTX-M-14 and CTX-M-15 β-lactamase by in vitro DNA shuffling. Antimicrobial Agents & Chemotherapy, 61, AAC.00891–AAC.00817.
Sheedy, C., Yau, K. Y., Hirama, T., Mackenzie, C. R., & Hall, J. C. (2006). Selection, characterization, and CDR shuffling of naive llama single-domain antibodies selected against auxin and their cross-reactivity with auxinic herbicides from four chemical families. Journal of Agricultural & Food Chemistry, 54, 3668–3678.
Schilling, J., Schoppe, J., & Plückthun, A. (2014). From DARPins to LoopDARPins: Novel LoopDARPin design allows the selection of low picomolar binders in a single round of ribosome display. Journal of Molecular Biology, 426, 691–721.
Rothe, A., Nathanielsz, A., Hosse, R. J., Oberhauser, F., Strandmann, E. P., Engert, A., Hudson, P. J., & Power, B. E. (2007). Selection of human anti-CD28 scFvs from a T-NHL related scFv library using ribosome display. Journal of Biotechnology, 130, 448–454.
Grimm, S., Salahshour, S., & Nygren, P. (2012). Monitored whole gene in vitro evolution of an anti-hRaf-1 affibody molecule towards increased binding affinity. New Biotechnology, 29, 534–542.
Buchanan, A., Ferraro, F., Rust, S., Sridharan, S., Franks, R., Dean, G., McCourt, M., Jermutus, L., & Minter, R. (2012). Improved drug-like properties of therapeutic proteins by directed evolution. Protein engineering, design & Selection: PEDS, 25, 631–638.
Matsuura, T., & Plückthun, A. (2003). Selection based on the folding properties of proteins with ribosome display. FEBS Letters, 539, 24–28.
Harel, I. N., & Benhar, I. (2012). Selection of antibodies from synthetic antibody libraries. Archives of Biochemistry & Biophysics, 526, 87–98.
Jiao, L., Liu, Y., Zhang, X., Liu, B., Zhang, C., & Liu, X. (2017). Site-saturation mutagenesis library construction and screening for specific broad-spectrum single-domain antibodies against multiple Cry1 toxins. Applied Microbiology and Biotechnology, 101, 6071–6082.
Sheedy, C., Roger MacKenzie, C., & Hall, J. C. (2007). Isolation and affinity maturation of hapten-specific antibodies. Biotechnology Advances, 25, 333–352.
Thom, G., Cockroft, A. C., Buchanan, A. G., Canclotti, C. J., Cohen, E. S., Lowne, D., Monk, P., Shorrock-Hart, C. P., Jermutus, L., & Minter, R. R. (2006). Probing a protein-protein interaction by in vitro evolution. Proceedings of the National Academy of Sciences of the United States of America, 103, 7619–7624.
Zahnd, C., Pecorari, F., Straumann, N., Wyler, E., & Plückthun, A. (2006). Selection and characterization of Her2 binding-designed ankyrin repeat proteins. Journal of Biological Chemistry, 281, 35167.
Stemmer, W. P. C. (1994). Rapid evolution of a protein in vitro by DNA shuffling. Nature, 370, 389–391.
Dreier, B., & Plückthun, A. (2011). Ribosome display: A technology for selecting and evolving proteins from large libraries. Methods in Molecular Biology, 687, 283–306.
Zhao, H., & Zha, W. (2006). In vitro ‘sexual’ evolution through the PCR-based staggered extension process (StEP). Nature Protocols, 1, 1865–1871.
Groves, M. A. T., & Osbourn, J. K. (2005). Applications of ribosome display to antibody drug discovery. Expert Opinion on Biological Therapy, 5, 125–135.
Zahnd, C., Spinelli, S., Luginbühl, B., Amstutz, P., Cambillau, C., & Plückthun, A. (2004). Directed in vitro evolution and crystallographic analysis of a peptide-binding single chain antibody fragment (scFv) with low picomolar affinity. Journal of Biological Chemistry, 279, 18870–18877.
Huang, R., Gorman, K. T., Vinci, C. R., Dobrovetsky, E., Graslund, S., & Kay, B. K. (2015). Streamlining the pipeline for generation of recombinant affinity reagents by integrating the affinity maturation step. International Journal of Molecular Sciences, 16, 23587–23603.
Zahnd, C., Sarkar, C. A., & Plückthun, A. (2010). Computational analysis of off-rate selection experiments to optimize affinity maturation by directed evolution. Protein Engineering Design & Selection Peds, 23, 175.
Luginbühl, B., Kanyo, Z., Jones, R. M., Fletterick, R. J., Prusiner, S. B., Cohen, F. E., Williamson, R. A., Burton, D. R., & Plückthun, A. (2006). Directed evolution of an anti-prion protein scFv fragment to an affinity of 1 pM and its structural interpretation. Journal of Molecular Biology, 363, 75–97.
Liu, J. Q., Ning, B., Liu, M., Sun, Y. A., Sun, Z. Y., Zhang, Y. H., Fan, X. J., Zhou, Z. J., & Gao, Z. X. (2012). Construction of ribosome display library based on lipocalin scaffold and screening anticalins with specificity for estradiol. Analyst, 137, 2470–2479.
Chin, S. E., Ferraro, F., Groves, M., Liang, M., Vaughan, T. J., & Dobson, C. L. (2015). Isolation of high-affinity, neutralizing anti-idiotype antibodies by phage and ribosome display for application in immunogenicity and pharmacokinetic analyses. Journal of Immunological Methods, 416, 49–58.
Dreier, B., & Plückthun, A. (2012). Rapid selection of high-affinity binders using ribosome display. Methods in Molecular Biology, 805, 261–286.
Chames, P., Van Regenmortel, M., Weiss, E., & Baty, D. (2009). Therapeutic antibodies: Successes, limitations and hopes for the future. British Journal of Pharmacology, 157, 220–233.
Jermutus, L., Honegger, A., Schwesinger, F., Hanes, J., & Plückthun, A. (2001). Tailoring in vitro evolution for protein affinity or stability. Proceedings of the National Academy of Sciences of the United States of America, 98, 75.
Heyduk, E., & Heyduk, T. (2014). Ribosome display enhanced by next generation sequencing: A tool to identify antibody-specific peptide ligands. Analytical Biochemistry, 464, 73–82.
Consortium, I. H. G. S. (2004). Finishing the euchromatic sequence of the human genome. Nature, 431, 931–945.
Galan, A., Comor, L., Horvatic, A., Kules, J., Guillemin, N., Mrljak, V., & Bhide, M. (2016). Library-based display technologies: where do we stand? Molecular Biosystems, 12, 2342–2358.
Stefan, N., Martinkillias, P., Wyssstoeckle, S., Honegger, A., Zangemeisterwittke, U., & Plückthun, A. (2011). DARPins recognizing the tumor-associated antigen EpCAM selected by phage and ribosome display and engineered for multivalency. Journal of Molecular Biology, 413, 826–843.
Dreier, B., Mikheeva, G., Belousova, N., Parizek, P., Boczek, E., Jelesarov, I., Forrer, P., Plückthun, A., & Krasnykh, V. (2011). Her2-specific multivalent adapters confer designed tropism to adenovirus for gene targeting. Journal of Molecular Biology, 405, 410–426.
Zellweger, F., Gasser, P., Brigger, D., Buschor, P., Vogel, M., & Eggel, A. (2017). A novel bispecific DARPin targeting FcgammaRIIB and FcepsilonRI-bound IgE inhibits allergic responses. Allergy, 72, 1174–1183.
Chen, F., Zhao, Y., Liu, M., Li, D., Wu, H., Chen, H., Zhu, Y., Luo, F., Zhong, J., Zhou, Y., Qi, Z., & Zhang, X. L. (2010). Functional selection of hepatitis C virus envelope E2-binding Peptide ligands by using ribosome display. Antimicrobial Agents and Chemotherapy, 54, 3355–3364.
Cheng, H., Chen, Y., Yang, Y., Chen, X., Guo, X., & Du, A. (2015) Characterization of anti-citrinin specific ScFvs selected from non-immunized mouse splenocytes by eukaryotic ribosome display. PLoS ONE, 10, e0131482.
Kanamori, T., Fujino, Y., & Ueda, T. (2014). PURE ribosome display and its application in antibody technology. Biochimica Et Biophysica Acta-Proteins and Proteomics, 1844, 1925–1932.
Gu, L. C., Li, C., Aach, J., Hill, D. E., Vidal, M., & Church, G. M. (2014). Multiplex single-molecule interaction profiling of DNA-barcoded proteins. Nature, 515, 554–557.
Li, Z., Uzawa, T., Zhao, H., Luo, S. C., Yu, H. H., Kobatake, E., & Ito, Y. (2013). In vitro selection of peptide aptamers using a ribosome display for a conducting polymer. Journal of Bioscience & Bioengineering, 117, 501–503.
Acknowledgements
We would like to thank colleagues working on display technologies in our laboratory for their assistance in the field. This work is supported by Grants from National Natural Science Foundation of China (No. 31470967).
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Conflict of interest
The authors declare no conflict of interest.
Research Involving Human Participants and/or Animals
This article does not contain any studies with human participants or animals performed by any of the authors.
Informed Consent
Informed consent was obtained from all individual participants included in the study.
Rights and permissions
About this article
Cite this article
Li, R., Kang, G., Hu, M. et al. Ribosome Display: A Potent Display Technology used for Selecting and Evolving Specific Binders with Desired Properties. Mol Biotechnol 61, 60–71 (2019). https://doi.org/10.1007/s12033-018-0133-0
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12033-018-0133-0