Bacterial signal peptides: structure, optimization, and applications

Authors

  • Esra Erkut undergraduate student (U of A)

DOI:

https://doi.org/10.29173/eureka28759

Keywords:

Signal sequence, Signal peptide, recombinant proteins, E. coli, Sec, Tat

Abstract

Bacterial signal peptides are N-terminal tags that direct proteins for export through one of various transport pathways. These signal peptides are highly important as they are the key determinants of transport, ensuring that the correct protein ends up at the correct pathway. While these peptides consist of three domains with well conserved biochemical properties, there still remains a large amount of diversity between the signal sequences for different proteins, transport pathways, and bacterial species. Recent advancements have allowed us to predict signal sequences and manipulate them in an attempt to optimize export efficiency. This knowledge can then be exploited in the field of recombinant protein production wherein bacterial species can be used to produce and secrete proteins of interest. By fusing the protein with an optimized signal peptide, the yield or rate of export can be improved. This review focuses on signal peptides for two primary transport pathways (Sec and Tat) in E. coli specifically, with an emphasis on applications and the production of recombinant proteins.

Downloads

Download data is not yet available.

References

References:

Alanen, H. I., Walker, K. L., Lourdes Velez Suberbie, M., Matos, C. F. R. O., Bönisch, S., Freedman, R. B., Keshavarz-Moore, E., Ruddock, L. W., & Robinson, C. (2015). Efficient export of human growth hormone, interferon α2b and antibody fragments to the periplasm by the Escherichia coli Tat pathway in the absence of prior disulfide bond formation. Biochimica et Biophysica Acta (BBA) - Molecular Cell Research, 1853(3), 756–763. https://doi.org/10.1016/j.bbamcr.2014.12.027

Bagos, P. G., Nikolaou, E. P., Liakopoulos, T. D., & Tsirigos, K. D. (2010). Combined prediction of Tat and Sec signal peptides with hidden Markov models. Bioinformatics, 26(22), 2811–2817. https://doi.org/10.1093/bioinformatics/btq530

Balasundaram, B., Harrison, S., & Bracewell, D. G. (2009). Advances in product release strategies and impact on bioprocess design. Trends in Biotechnology, 27(8), 477–485. https://doi.org/10.1016/j.tibtech.2009.04.004

Bendtsen, J. D., Nielsen, H., Widdick, D., Palmer, T., & Brunak, S. (2005). Prediction of twin-arginine signal peptides. BMC Bioinformatics, 6(1), 167. https://doi.org/10.1186/1471-2105-6-167

Blaudeck, N., Kreutzenbeck, P., Freudl, R., & Sprenger, G. A. (2003). Genetic Analysis of Pathway Specificity during Posttranslational Protein Translocation across the Escherichia coli Plasma Membrane. Journal of Bacteriology, 185(9), 2811–2819. https://doi.org/10.1128/JB.185.9.2811-2819.2003

Bogsch, E., Brink, S., & Robinson, C. (1997). Pathway specificity for a ΔpH-dependent precursor thylakoid lumen protein is governed by a 'sec-avoidance’ motif in the transfer peptide and a 'sec-incompatible’ mature protein. The EMBO Journal, 16(13), 3851–3859. https://doi.org/10.1093/emboj/16.13.3851

Bowers, C. W., Lau, F., & Silhavy, T. J. (2003). Secretion of LamB-LacZ by the Signal Recognition Particle Pathway of Escherichia coli. Journal of Bacteriology, 185(19), 5697–5705. https://doi.org/10.1128/JB.185.19.5697-5705.2003

Brink, S., Bogsch, E. G., Edwards, W. R., Hynds, P. J., & Robinson, C. (1998). Targeting of thylakoid proteins by the ΔpH-driven twin-arginine translocation pathway requires a specific signal in the hydrophobic domain in conjunction with the twin-arginine motif. FEBS Letters, 434(3), 425–430. https://doi.org/10.1016/S0014-5793(98)01028-X

Brockmeier, U., Caspers, M., Freudl, R., Jockwer, A., Noll, T., & Eggert, T. (2006). Systematic Screening of All Signal Peptides from Bacillus subtilis: A Powerful Strategy in Optimizing Heterologous Protein Secretion in Gram-positive Bacteria. Journal of Molecular Biology, 362(3), 393–402. https://doi.org/10.1016/j.jmb.2006.07.034

Browning, D. F., Richards, K. L., Peswani, A. R., Roobol, J., Busby, S. J. W., & Robinson, C. (2017). Escherichia coli “TatExpress” strains super-secrete human growth hormone into the bacterial periplasm by the Tat pathway. Biotechnology and Bioengineering, 114(12), 2828–2836. https://doi.org/10.1002/bit.26434

Chaddock, A. m., Mant, A., Karnauchov, I., Brink, S., Herrmann, R. g., Klösgen, R. b., & Robinson, C. (1995). A new type of signal peptide: Central role of a twin-arginine motif in transfer signals for the delta pH-dependent thylakoidal protein translocase. The EMBO Journal, 14(12), 2715–2722. https://doi.org/10.1002/j.1460-2075.1995.tb07272.x

Chen, H., Kim, J., & Kendall, D. A. (1996). Competition between functional signal peptides demonstrates variation in affinity for the secretion pathway. Journal of Bacteriology, 178(23), 6658–6664. https://doi.org/10.1128/jb.178.23.6658-6664.1996

Choi, J. H., Jeong, K. J., Kim, S. C., & Lee, S. Y. (2000). Efficient secretory production of alkaline phosphatase by high cell density culture of recombinant Escherichia coli using the Bacillus sp. Endoxylanase signal sequence. Applied Microbiology and Biotechnology, 53(6), 640–645. https://doi.org/10.1007/s002530000334

Chou, Y.-T., & Gierasch, L. M. (2005). The Conformation of a Signal Peptide Bound by Escherichia coli Preprotein Translocase SecA. Journal of Biological Chemistry, 280(38), 32753–32760. https://doi.org/10.1074/jbc.M507532200

Consortium, T. U. (2019). UniProt: A worldwide hub of protein knowledge. Nucleic Acids Research, 47(D1), D506–D515. https://doi.org/10.1093/nar/gky1049

Crane, J. M., & Randall, L. L. (2017). The Sec System: Protein Export in Escherichia coli. EcoSal Plus, 7(2). https://doi.org/10.1128/ecosalplus.ESP-0002-2017

Cristóbal, S., de Gier, J.-W., Nielsen, H., & von Heijne, G. (1999). Competition between Sec- and TAT-dependent protein translocation in Escherichia coli. The EMBO Journal, 18(11), 2982–2990. https://doi.org/10.1093/emboj/18.11.2982

Degering, C., Eggert, T., Puls, M., Bongaerts, J., Evers, S., Maurer, K.-H., & Jaeger, K.-E. (2010). Optimization of Protease Secretion in Bacillus subtilis and Bacillus licheniformis by Screening of Homologous and Heterologous Signal Peptides. Applied and Environmental Microbiology, 76(19), 6370–6376. https://doi.org/10.1128/AEM.01146-10

Emr, S. D., Schwartz, M., & Silhavy, T. J. (1978). Mutations altering the cellular localization of the phage lambda receptor, an Escherichia coli outer membrane protein. Proceedings of the National Academy of Sciences, 75(12), 5802–5806. https://doi.org/10.1073/pnas.75.12.5802

Ferrer-Miralles, N., Domingo-Espín, J., Corchero, J. L., Vázquez, E., & Villaverde, A. (2009). Microbial factories for recombinant pharmaceuticals. Microbial Cell Factories, 8(1), 17. https://doi.org/10.1186/1475-2859-8-17

Freudl, R. (2018). Signal peptides for recombinant protein secretion in bacterial expression systems. Microbial Cell Factories, 17(1), 52. https://doi.org/10.1186/s12934-018-0901-3

Gelis, I., Bonvin, A. M. J. J., Keramisanou, D., Koukaki, M., Gouridis, G., Karamanou, S., Economou, A., & Kalodimos, C. G. (2007). Structural Basis for Signal-Sequence Recognition by the Translocase Motor SecA as Determined by NMR. Cell, 131(4), 756–769. https://doi.org/10.1016/j.cell.2007.09.039

Georgiou, G., & Segatori, L. (2005). Preparative expression of secreted proteins in bacteria: Status report and future prospects. Current Opinion in Biotechnology, 16(5), 538–545. https://doi.org/10.1016/j.copbio.2005.07.008

Gottesman, S. (1996). Proteases and Their Targets in Escherichia Coli. Annual Review of Genetics, 30(1), 465–506. https://doi.org/10.1146/annurev.genet.30.1.465

Goudenège, D., Avner, S., Lucchetti-Miganeh, C., & Barloy-Hubler, F. (2010). CoBaltDB: Complete bacterial and archaeal orfeomes subcellular localization database and associated resources. BMC Microbiology, 10(1), 88. https://doi.org/10.1186/1471-2180-10-88

Green, E. R., & Mecsas, J. (2016). Bacterial Secretion Systems – An overview. Microbiology Spectrum, 4(1). https://doi.org/10.1128/microbiolspec.VMBF-0012-2015

Guerrero Montero, I., Richards, K. L., Jawara, C., Browning, D. F., Peswani, A. R., Labrit, M., Allen, M., Aubry, C., Davé, E., Humphreys, D. P., Busby, S. J. W., & Robinson, C. (2019). Escherichia coli “TatExpress” strains export several g/L human growth hormone to the periplasm by the Tat pathway. Biotechnology and Bioengineering, 116(12), 3282–3291. https://doi.org/10.1002/bit.27147

Hiller, K., Grote, A., Scheer, M., Münch, R., & Jahn, D. (2004). PrediSi: Prediction of signal peptides and their cleavage positions. Nucleic Acids Research, 32(suppl_2), W375–W379. https://doi.org/10.1093/nar/gkh378

Inouye, S., Soberon, X., Franceschini, T., Nakamura, K., Itakura, K., & Inouye, M. (1982). Role of positive charge on the amino-terminal region of the signal peptide in protein secretion across the membrane. Proceedings of the National Academy of Sciences, 79(11), 3438–3441. https://doi.org/10.1073/pnas.79.11.3438

Isaksson, O. G. P., Eden, S., & Jansson, J. (1985). Mode of Action of Pituitary Growth Hormone on Target Cells. Annual Review of Physiology, 47(1), 483–499. https://doi.org/10.1146/annurev.ph.47.030185.002411

Ismail, N. F., Hamdan, S., Mahadi, N. M., Murad, A. M. A., Rabu, A., Bakar, F. D. A., Klappa, P., & Illias, R. Md. (2011). A mutant l-asparaginase II signal peptide improves the secretion of recombinant cyclodextrin glucanotransferase and the viability of Escherichia coli. Biotechnology Letters, 33(5), 999–1005. https://doi.org/10.1007/s10529-011-0517-8

Joly, J. C., Leung, W. S., & Swartz, J. R. (1998). Overexpression of Escherichia coli oxidoreductases increases recombinant insulin-like growth factor-I accumulation. Proceedings of the National Academy of Sciences, 95(6), 2773–2777. https://doi.org/10.1073/pnas.95.6.2773

Käll, L., Krogh, A., & Sonnhammer, E. L. L. (2007). Advantages of combined transmembrane topology and signal peptide prediction—The Phobius web server. Nucleic Acids Research, 35(suppl_2), W429–W432. https://doi.org/10.1093/nar/gkm256

Kumar, S., Stecher, G., Li, M., Knyaz, C., & Tamura, K. (2018). MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. Molecular Biology and Evolution, 35(6), 1547–1549. https://doi.org/10.1093/molbev/msy096

Low, K. O., Muhammad Mahadi, N., & Md. Illias, R. (2013). Optimisation of signal peptide for recombinant protein secretion in bacterial hosts. Applied Microbiology and Biotechnology, 97(9), 3811–3826. https://doi.org/10.1007/s00253-013-4831-z

Lüke, I., Handford, J. I., Palmer, T., & Sargent, F. (2009). Proteolytic processing of Escherichia coli twin-arginine signal peptides by LepB. Archives of Microbiology, 191(12), 919–925. https://doi.org/10.1007/s00203-009-0516-5

Mergulhão, F. J. M., Summers, D. K., & Monteiro, G. A. (2005). Recombinant protein secretion in Escherichia coli. Biotechnology Advances, 23(3), 177–202. https://doi.org/10.1016/j.biotechadv.2004.11.003

Mhiri, S., Mezghani, M., Mellouli, L., Ben Ali, M., Belguith, K., & Bejar, S. (2000). Efficient synthetic signal peptides for Streptomyces. Biotechnology Letters, 22(16), 1305–1310. https://doi.org/10.1023/A:1005678311475

Molloy, M. P., Herbert, B. R., Slade, M. B., Rabilloud, T., Nouwens, A. S., Williams, K. L., & Gooley, A. A. (2000). Proteomic analysis of the Escherichia coli outer membrane. European Journal of Biochemistry, 267(10), 2871–2881. https://doi.org/10.1046/j.1432-1327.2000.01296.x

Mori, H., Araki, M., Hikita, C., Tagaya, M., & Mizushima, S. (1997). The hydrophobic region of signal peptides is involved in the interaction with membrane-bound SecA. Biochimica et Biophysica Acta (BBA) - Biomembranes, 1326(1), 23–36. https://doi.org/10.1016/S0005-2736(97)00004-7

Nesmeyanova, M. A., Karamyshev, A. L., Karamysheva, Z. N., Kalinin, A. E., Ksenzenko, V. N., & Kajava, A. V. (1997). Positively charged lysine at the N-terminus of the signal peptide of the Escherichia coli alkaline phosphatase provides the secretion efficiency and is involved in the interaction with anionic phospholipids. FEBS Letters, 403(2), 203–207. https://doi.org/10.1016/S0014-5793(97)00052-5

Palmer, T., & Berks, B. C. (2012). The twin-arginine translocation (Tat) protein export pathway. Nature Reviews Microbiology, 10(7), 483–496. https://doi.org/10.1038/nrmicro2814

Patra, A. K., Mukhopadhyay, R., Mukhija, R., Krishnan, A., Garg, L. C., & Panda, A. K. (2000). Optimization of Inclusion Body Solubilization and Renaturation of Recombinant Human Growth Hormone from Escherichia coli. Protein Expression and Purification, 18(2), 182–192. https://doi.org/10.1006/prep.1999.1179

Peng, C., Shi, C., Cao, X., Li, Y., Liu, F., & Lu, F. (2019). Factors Influencing Recombinant Protein Secretion Efficiency in Gram-Positive Bacteria: Signal Peptide and Beyond. Frontiers in Bioengineering and Biotechnology, 7. https://doi.org/10.3389/fbioe.2019.00139

Petersen, T. N., Brunak, S., von Heijne, G., & Nielsen, H. (2011). SignalP 4.0: Discriminating signal peptides from transmembrane regions. Nature Methods, 8(10), 785–786. https://doi.org/10.1038/nmeth.1701

Pooley, H. M., Merchante, R., & Karamata, D. (1996). Overall Protein Content and Induced Enzyme Components of the Periplasm of Bacillus subtilis. Microbial Drug Resistance, 2(1), 9–15. https://doi.org/10.1089/mdr.1996.2.9

Rose, R. W., Brüser, T., Kissinger, J. C., & Pohlschröder, M. (2002). Adaptation of protein secretion to extremely high-salt conditions by extensive use of the twin-arginine translocation pathway. Molecular Microbiology, 45(4), 943–950. https://doi.org/10.1046/j.1365-2958.2002.03090.x

Rusch, S. L., & Kendall, D. A. (2007). Interactions That Drive Sec-Dependent Bacterial Protein Transport. Biochemistry, 46(34), 9665–9673. https://doi.org/10.1021/bi7010064

Spadiut, O., Capone, S., Krainer, F., Glieder, A., & Herwig, C. (2014). Microbials for the production of monoclonal antibodies and antibody fragments. Trends in Biotechnology, 32(1), 54–60. https://doi.org/10.1016/j.tibtech.2013.10.002

Terpe, K. (2006). Overview of bacterial expression systems for heterologous protein production: From molecular and biochemical fundamentals to commercial systems. Applied Microbiology and Biotechnology, 72(2), 211–222. https://doi.org/10.1007/s00253-006-0465-8

Tullman-Ercek, D., DeLisa, M. P., Kawarasaki, Y., Iranpour, P., Ribnicky, B., Palmer, T., & Georgiou, G. (2007). Export Pathway Selectivity of Escherichia coli Twin Arginine Translocation Signal Peptides. Journal of Biological Chemistry, 282(11), 8309–8316. https://doi.org/10.1074/jbc.M610507200

Ultsch, M. H., Somers, W., Kossiakoff, A. A., & de Vos, A. M. (1994). The Crystal Structure of Affinity-matured Human Growth Hormone at 2 Å Resolution. Journal of Molecular Biology, 236(1), 286–299. https://doi.org/10.1006/jmbi.1994.1135

Wong, W. K. R., & Sutherland, M. L. (1993). Excretion of heterologous proteins from e. Coli (United States Patent No. US5223407A). https://patents.google.com/patent/US5223407A/en

Zhou, Y., Liu, P., Gan, Y., Sandoval, W., Katakam, A. K., Reichelt, M., Rangell, L., & Reilly, D. (2016). Enhancing full-length antibody production by signal peptide engineering. Microbial Cell Factories, 15(1), 47. https://doi.org/10.1186/s12934-016-0445-3

Downloads

Published

2021-08-27 — Updated on 2021-08-27

Versions

How to Cite

Erkut, E. (2021). Bacterial signal peptides: structure, optimization, and applications. Eureka, 6(1). https://doi.org/10.29173/eureka28759

Issue

Vol. 6 No. 1 (2021)

Section

Reviews

License

Copyright (c) 2021 Eureka

Creative Commons License

This work is licensed under a Creative Commons Attribution 4.0 International License.

By signing the Eureka publication agreement, authors agree to the following: 

  • The work has not been previously published in any format; 
  • Eureka is granted the royalty-free right to publish and disseminate the work in current and future formats; 
  • The work will be published in Eureka under a Creative Commons license. Eureka encourages authors to publish the work under a Creative Commons Attribution 4.0 International license (CC BY 4.0) that allows others to distribute, tweak, and build upon the work, even commercially, as long as they credit the Author(s) for the original creation. 

Authors may however choose to have their work distributed under any of the Creative Commons licenses currently available by specifying their preferred license in the publication agreement. A description of the Creative Commons licenses is available here: https://creativecommons.org/licenses/ 

  • Authors retain their copyright, including the right to subsequently publish or disseminate their work elsewhere, provided that they make reasonable efforts to ensure that the publication in Eureka is acknowledged. 
  • Authors agree to determine, prior to publication, whether it is necessary to obtain permissions from any third party who hold rights with respect to any photographs, illustrations, drawings, text, or any other material (“third party work”) to be published in connection with your work. Copyright permission will not be necessary if the use is determined to be fair dealing, if the work is in the public domain, or if the rights-holder has granted a Creative Commons or similar license. 
  • All co-authors and investigators (e.g. faculty supervisors) with claims to the intellectual property have read and signed the agreement, thereby providing their consent for the submission to be published in Eureka. 

Unless otherwise specified, authors guarantee that all parts of the submission are the author’s original work. Submissions containing evidence of plagiarism will not be eligible for publication.