In silico analysis of different signal peptides to discover a panel of appropriate signal peptides for secretory production of Interferon-beta 1b in Escherichia coli
Signal peptides (SPs) are one of the most important factors for suitable secretion of the recombinant heterologous proteins in Escherichia coli (E. coli). The objective of this study was to identify a panel of signal peptides (among the 90 biologically active SPs) required for the secretory production of interferon-beta 1b (IFN-beta 1b) recombinant protein into the periplasmic space of E. coli host. In the initial step, after predicting the accurate locations of the cleavage sites of signal peptides and their discrimination scores using SignalP 4.1 server, 31 SPs were eliminated from further analysis because their discrimination scores were less than 0.5 or their cleavage sites were inappropriately located. Therefore, only 59 SPs could be theoretically applied to secrete IFN-beta 1b into the periplasmic space of E. coli. The physico-chemical and the solubility properties, which are necessary parameters for selecting appropriate SPs, were predicted using ProtParam and SOLpro servers using the 59 remaining signal peptides. The final subcellular localization of IFN-beta 1b in combination with different SPs was predicted using ProtComB server. Consequently, according to the ranking of 59 confirmed SPs, the obtained results revealed that SPs Flagellar P-ring protein (flgI), Glucan
1,3-beta-glucosidase I/II (EXG1) and outer membrane protein C (OmpC) were theoretically the most potent
and desirable SPs for secretion of recombinant IFN-beta 1b into the periplasmic space of E. coli. For further studies in the future, the experimental investigations on the obtained results will be considered.
Babaeipour V, Shojaosadati SA, Maghsoudi N (2013) Maximizing production of human interferon-γ in HCDC of recombinant E. coli. Iran J Pharm Res, 12, 563-572.
Bagos PG, Nikolaou EP, Liakopoulos TD, Tsirigos KD (2010) Combined prediction of Tat and Sec signal peptides with hidden Markov models. Bioinformatics, 26(22), 2811-2817.
Baneyx F (1999) Recombinant protein expression in Escherichia coli. Curr Opin Biotechnol, 10, 411-421.
Baneyx F, Mujacic M (2004) Recombinant protein folding and misfolding in Escherichia coli. Nat Biotechnol, 22(11), 1399–1408.
Baradaran A, Sieo CC, Foo HL, Illias RM, Yusoff K, Rahim RA (2013) Cloning and in silico characterization of two signal peptides from Pediococcus pentosaceus and their function for the secretion of heterologous protein in Lactococcus lactis. Biotechnol Lett, 35(2), 233–238.
Chen H, Kim J, Kendall DA (1996) Competition between functional signal peptides demonstrates variation in affinity for the secretion pathway. J Bacteriol, 178(23), 6658–6664.
Choi J, Lee S (2004) Secretory and extracellular production of recombinant proteins using Escherichia coli. Appl Microbiol Biotechnol, 64(5), 625–635.
Cohen B, Parkin J (2001) An overview of the immune system. Lancet, 357(9270), 1777-1789.
Dalton AC, Barton WA (2014) Over-expression of secreted proteins from mammalian cell lines. Protein Science : A Publication of the Protein Society, 23(5), 517-525. doi:http://doi.org/10.1002/pro.2439
Dyrløv Bendtsen J, Nielsen H, von Heijne G, Brunak S (2004) Improved prediction of signal peptides: SignalP 3.0. J Mol Biol, 340(4), 783–795.
Ekins S, Mestres J, Testa B (2007) In silico pharmacology for drug discovery: methods for virtual ligand screening and profiling. British Journal of Pharmacology, 152(1), 9-20.
Gasteiger E, Bairoch A, Sanchez JC, William, KL, Wilkins MR, Appel RD, Hochstrasser DF (2005) Protein identification and analysis tools in the ExPASy server. Methods Mol Biol, 112, 531-552.
Hartman GD, Egbertson MS, Halczenko W, Laswell WL, Duggan ME, Smith RL, et al. (1992) Non-peptide fibrinogen receptor antagonists. 1. Discovery and design of exosite inhibitors. J Med Chem, 35, 4640–4642.
Klee EW, Ellis LBM (2005) Evaluating eukaryotic secreted protein prediction BMC Bioinformatics, 6, 256.
Kolb-Maurer A, Goebeler M, Maurer M (2015) Cutaneous Adverse Events Associated with Interferon-beta Treatment of Multiple Sclerosis. Int J Mol Sci, 16(7), 14951-14960. doi:10.3390/ijms160714951
Krishna Rao DV, Ramu CT, Venkateswara Rao J, Narasu ML, Bhujanga Rao AKS (2009) Cloning, High Expression and Purification of Recombinant Human Intereferon-β-1b in Escherichia coli. Appl Biochem Biotechnol, 158, 140–154.
Magnan CN, Randall A, Baldi P (2009) SOLpro: accurate sequencebased prediction of protein solubility. Bioinformatics, 25(17), 2200–2207.
Marziniak M, Meuth S (2014) Current perspectives on interferon Beta-1b for the treatment of multiple sclerosis. Adv Ther, 31(9), 915-931. doi:10.1007/s12325-014-0149-1
Mergulha˜o FJM, Summers DK, Monteiro GA (2005) Recombinant protein secretion in Escherichia coli. Biotechnol Adv, 23, 177–202.
Mobasher MA, Ghasemi Y, Montazeri-Najafabady N, Tahzibi A (2016) Expression of recombinant IFN beta 1-b a comparison between soluble and insoluble forms. Minerva Biotecnologica, 28(1), 39-43.
Morowvat MH, Babaeipour V, Rajabi-Memari H, Vahidi H, Maghsoudi N (2014) Overexpression of Recombinant Human Beta Interferon (rhINF-beta) in Periplasmic Space of Escherichia coli. Iran J Pharm Res, 13(Suppl), 151-160.
Petersen TN, Brunak S, von Heijne G, Nielsen H (2011) SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods, 8(10), 785-786. doi:10.1038/nmeth.1701
Pratap J, Dikshit K (1998) Effect of signal peptide changes on the extracellular processing of streptokinase from Escherichia coli: requirement for secondary structure at the cleavage junction. Mol Gen Genet MGG, 258(4), 326–333.
Ramanan RN, Tik WB, Memari HR, Azaman SNA, Ling TC, Tey BT, et al. (2010) Effect of promoter strength and signal sequence on the periplasmic expression of human interferon-a2b in Escherichia coli. Afr J Biotechnol, 9(3), 285–292.
Runkel L, Meier W, Pepinsky RB, Karpusas M, Whitty A, Kimball K, et al. (1998) Structural and functional differences between glycosylated and non-glycosylated forms of human interferon-beta (IFN-beta). Pharm Res, 15, 641-649.
Sen GC, Lengyel P (1992) The Interferon system. J Biol Chem, 267(8), 5017-5020.
Sørensen PS (2010) Interferon-beta-1a: Therapeutic effects, tolerability, current and future status in multiple sclerosis. Hot Topics Neurol Psychiatr, 3, 7-16.
Talele TT, Khedkar SA, Rigby AC (2010) Successful Applications of Computer Aided Drug Discovery: Moving Drugs from Concept to the Clinic. Current Topics in Medicinal Chemistry, 10(1), 127-141. doi:10.2174/156802610790232251
Van Drie JH (2007) Computer-aided drug design: the next 20 years. J Comput Aided Mol Des, 21, 591–601.
Ventura S, Villaverde A (2006) Protein quality in bacterial inclusion bodies. . Trends Biotechnol, 24, 179–185.
Yoon S, Kim S, Kim JF (2010) Secretory production of recombinant proteins in Escherichia coli. Recent Pat Biotechnol, 4, 23–29.
Zamani M, Nezafat N, Negahdaripour M, Dabbagh F, Ghasemi Y (2015) In Silico Evaluation of Different Signal Peptides for the Secretory Production of Human Growth Hormone in E. coli. International Journal of Peptide Research and Therapeutics, 21(3), 261-268.
Acta Biochimica Polonica is an OpenAccess quarterly and publishes four issues a year. All contents are distributed under the Creative Commons Attribution-ShareAlike 4.0 International (CC BY 4.0) license. Everybody may use the content following terms: Attribution — You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use.
Copyright for all published papers © stays with the authors.
Copyright for the journal: © Polish Biochemical Society.