Abstract
Anabaena variabilis double mutant (C503S/C565S) phenylalanine ammonia-lyase (PAL) is an appealing enzyme in the enzyme-replacement therapy of phenylketonuria. Yet abundant production of this enzyme has been of concern for industrial production. In this study, we have characterized 1175 bacterial signal peptides (SPs) and identified the most efficient ones for the excretory production of mutant AvPAL. Analysis by SignalP 4.1 revealed that more than 61% of SPs had a D-score greater than 0.7, denoting to be highly efficient. The optimum length of a bacterial SP was 25–30. The preferable net positive charge and the second residue of N-region were + 2 and Lys/Arg, respectively. Highly efficient SPs possessed 3–5 Leus in their H-region and A/L/VXA-FF cleavage site. Highly efficient SPs were from Escherichia coli, corroborating the necessity of an agreement between SPs and the host. Physiochemical characterization of mutant AvPAL conjugates via ProtParam and PROSOII, revealed that ~ 99.5% of proteins would not be entraped in inclusion bodies. Secretory pathways were identified by EffectiveDB and more than 98% of SPs were cleavable. Chimeras were modeled using the I-TASSER program, being evaluated by the Ramachandran plots. The mRNA secondary structure of mutant AvPAL upon linkage to SPs was assessed using the mfold program. It was shown that the linkage of a SP does not affect mutant AvPAL’s stability at the protein or mRNA level. AllergenFP tool demonstrated that chimeras were not allergen. SPs, including FMF4_ECOLX, E2BB_ECOLX, and LPTA_ECOLI exhibited the highest propensity for secretion and appropriate features in all analyses.
Similar content being viewed by others
Abbreviations
- Phe:
-
Phenylalanine
- PAL:
-
Phenylalanine Ammonia Lyase
- PKU:
-
Phenylketonuria
- t-CA:
-
Trans-cinnamic acid
- LNAA:
-
Large neutral amino acid
- SP:
-
Signal peptide
- HMM:
-
Hidden Markov model
References
Aydaş SB, Ozturk S, Aslım B (2013) Phenylalanine ammonia lyase (PAL) enzyme activity and antioxidant properties of some cyanobacteria isolates. Food Chem 136(1):164–169. https://doi.org/10.1016/j.foodchem.2012.07.119
Babich OO, Pokrovsky VS, Anisimova NY, Sokolov NN, Prosekov AY (2013) Recombinant l-phenylalanine ammonia lyase from Rhodosporidium toruloides as a potential anticancer agent. Biotechnol Appl Biochem 60(3):316–322. https://doi.org/10.1002/bab.1089
Beena K, Udgaonkar JB, Varadarajan R (2004) Effect of signal peptide on the stability and folding kinetics of maltose binding protein. Biochemistry 43(12):3608–3619. https://doi.org/10.1021/bi0360509
Bell SM, Wendt DJ, Zhang Y, Taylor TW, Long S, Tsuruda L, Zhao B, Laipis P, Fitzpatrick PA (2017) Formulation and PEGylation optimization of the therapeutic PEGylated phenylalanine ammonia lyase for the treatment of phenylketonuria. PloS one 12(3):e0173269. https://doi.org/10.1371/journal.pone.0173269
Bendtsen JD, Nielsen H, von Heijne G, Brunak S (2004) Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 340(4):783–795. https://doi.org/10.1016/j.jmb.2004.05.028
Blau N, Longo N (2015) Alternative therapies to address the unmet medical needs of patients with phenylketonuria. Expert Opin Pharmacother 6(6):791–800. https://doi.org/10.1517/14656566.2015.1013030
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. J Mol Biol 362(3):393–402. https://doi.org/10.1016/j.jmb.2006.07.034
Büttner D (2012) Protein export according to schedule: architecture, assembly, and regulation of type III secretion systems from plant-and animal-pathogenic bacteria. Microbiol Mol Biol Rev 76(2):262–310. https://doi.org/10.1128/MMBR.05017-11
Chan W-C, Liang P-H, Shih Y-P, Yang U-C, Lin W-c, Hsu C-N (2010) Learning to predict expression efficacy of vectors in recombinant protein production. BMC Bioinform 11(1):S21. https://doi.org/10.1186/1471-2105-11-S1-S21
Chang CCH, Song J, Tey BT, Ramanan RN (2013) Bioinformatics approaches for improved recombinant protein production in Escherichia coli: protein solubility prediction. Brief Bioinform 15(6):953–962. https://doi.org/10.1093/bib/bbt057
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. https://doi.org/10.1128/jb.178.23.6658-6664.1996
Choo KH, Ranganathan S (2008) Flanking signal and mature peptide residues influence signal peptide cleavage BMC Bioinform 9(12):S15. https://doi.org/10.1186/1471-2105-9-S12-S15
Choo KH, Tan TW, Ranganathan S (2005) SPdb–a signal peptide database. BMC Bioinform 6(1):249. https://doi.org/10.1186/1471-2105-6-249
Chou K-C (2002) Prediction of protein signal sequences. Curr Prot Pept Sci 3(6):615–622. https://doi.org/10.2174/1389203023380468
Cui J-D, Zhang S, Sun L-M (2012) Cross-linked enzyme aggregates of phenylalanine ammonia lyase: novel biocatalysts for synthesis of L-phenylalanine. Appl Biochem Biotechnol 167(4):835–844. https://doi.org/10.1007/s12010-012-9738-0
Cui JD, Qiu JQ, Fan XW, Jia SR, Tan ZL (2014) Biotechnological production and applications of microbial phenylalanine ammonia lyase: a recent review. Crit Rev Biotechnol 34(3):258–268. https://doi.org/10.3109/07388551.2013.791660
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. Appl Environ Microbiol 76(19):6370–6376. https://doi.org/10.1128/AEM.01146-10
Dimitrov I, Naneva L, Doytchinova I, Bangov I (2013) AllergenFP: allergenicity prediction by descriptor fingerprints. Bioinformatics 30(6):846–851. https://doi.org/10.1093/bioinformatics/btt619
Duffy J, Patham B, Mensa-Wilmot K (2010) Discovery of functional motifs in h-regions of trypanosome signal sequences. Biochem J 426(2):135–145. https://doi.org/10.1042/BJ20091277
Eichinger V, Nussbaumer T, Platzer A, Jehl M-A, Arnold R, Rattei T (2015) EffectiveDB—updates and novel features for a better annotation of bacterial secreted proteins and Type III, IV, VI secretion systems. Nucleic Acids Res 44(D1):D669–D674. https://doi.org/10.1093/nar/gkv1269
Fakruddin M, Mohammad Mazumdar R, Bin Mannan KS, Chowdhury A, Hossain MN (2012) Critical factors affecting the success of cloning, expression, and mass production of enzymes by recombinant E. coli. ISRN Biotechnol. https://doi.org/10.5402/2013/590587
Futatsumori-Sugai M, Tsumoto K (2010) Signal peptide design for improving recombinant protein secretion in the baculovirus expression vector system. Biochem Biophys Res Commun 391(1):931–935. https://doi.org/10.1016/j.bbrc.2009.11.167
Gao J, Zhang S, Cai F, Zheng X, Lin N, Qin X, Ou Y, Gu X, Zhu X, Xu Y (2012) Characterization, and expression profile of a phenylalanine ammonia lyase gene from Jatropha curcas L. Mol Biol Rep 39(4):3443–3452. https://doi.org/10.1007/s11033-011-1116-4
Garg SG, Gould SB (2016) The role of charge in protein targeting evolution. Trends Cell Biol 26(12):894–905. https://doi.org/10.1016/j.tcb.2016.07.001
Gasteiger E, Hoogland C, Gattiker A, Wilkins MR, Appel RD, Bairoch A (2005) Protein identification and analysis tools on the ExPASy server. The proteomics protocols handbook. Springer, New York 571–607
Geukens N, Frederix F, Reekmans G, Lammertyn E, Van Mellaert L, Dehaen W, Maes G, Anné J (2004) Analysis of type I signal peptidase affinity and specificity for preprotein substrates. Biochem Biophys Res Commun 314(2):459–467. https://doi.org/10.1016/j.bbrc.2003.12.122
Green ER, Mecsas J (2016) Bacterial secretion systems–an overview. Microbiol Spectr 4(1). https://doi.org/10.1128/microbiolspec.VMBF-0012-2015
Hegde RS, Bernstein HD (2006) The surprising complexity of signal sequences. Trends Biochem Sci 31(10):563–571. https://doi.org/10.1016/j.tibs.2006.08.004
Heng CK (2009) Bioinformatic analysis of bacterial and eukaryotic amino-terminal signal peptides
Hiss JA, Schneider G (2009) Architecture, function and prediction of long signal peptides. Brief Bioinform 10(5):569–578. https://doi.org/10.1093/bib/bbp030
Ikeda K, Schiltz E, Fujii T, Takahashi M, Mitsui K, Kodera Y, Matsushima A, Inada Y, Schulz G, Nishimura H (2005) Phenylalanine ammonia-lyase modified with polyethylene glycol: potential therapeutic agent for phenylketonuria. Amino Acids 29(3):283–287. https://doi.org/10.1007/s00726-005-0218-5
Ismail NF, Hamdan S, Mahadi NM, Murad AMA, Rabu A, Bakar FDA, Klappa P, Illias RM (2011) A mutant L-asparaginase II signal peptide improves the secretion of recombinant cyclodextrin glucanotransferase and the viability of Escherichia coli. Biotechnol Lett 33(5):999–1005. https://doi.org/10.1007/s10529-011-0517-8
Ivankov DN, Payne SH, Galperin MY, Bonissone S, Pevzner PA, Frishman D (2013) How many signal peptides are there in bacteria? Environ Microbiol 15(4):983–990. https://doi.org/10.1111/1462-2920.12105
Jonet MA, Mahadi NM, Murad AMA, Rabu A, Bakar FDA, Rahim RA, Low KO, Illias RM (2012) Optimization of a heterologous signal peptide by site-directed mutagenesis for improved secretion of recombinant proteins in Escherichia coli. J Mol Microbiol Biotechnol 22(1):48–58. https://doi.org/10.1159/000336524
Joshi SN, Butler DC, Messer A (2012) Fusion to a highly charged proteasomal retargeting sequence increases soluble cytoplasmic expression and efficacy of diverse anti-synuclein intrabodies. MAbs, Taylor & Francis, Didcot
Kim SJ, Mitra D, Salerno JR, Hegde RS (2002) Signal sequences control gating of the protein translocation channel in a substrate-specific manner. Dev Cell 2(2):207–217. https://doi.org/10.1016/S1534-5807(01)00120-4
Kober L, Zehe C, Bode J (2013) Optimized signal peptides for the development of high expressing CHO cell lines. Biotechnol Bioeng 110(4):1164–1173. https://doi.org/10.1002/bit.24776
Kong J-Q (2015) Phenylalanine ammonia-lyase, a key component used for phenylpropanoids production by metabolic engineering. RSC Adv 5(77):62587–62603. https://doi.org/10.1039/c5ra08196c
Kulothungan SR, Das M, Johnson M, Ganesh C, Varadarajan R (2009) Effect of crowding agents, signal peptide, and chaperone SecB on the folding and aggregation of E. coli maltose binding protein. Langmuir 25(12):6637–6648. https://doi.org/10.1021/la900198h
Kvam E, Sierks MR, Shoemaker CB, Messer A (2010) Physico-chemical determinants of soluble intrabody expression in mammalian cell cytoplasm. Prot Eng Des Sel 23(6):489–498. https://doi.org/10.1093/protein/gzq022
Laskowski RA (2007) Enhancing the functional annotation of PDB structures in PDBsum using key figures extracted from the literature. Bioinformatics 23(14): 1824–1827. https://doi.org/10.1093/bioinformatics/btm085
Laskowski RA, Jabłońska J, Pravda L, Vařeková RS, Thornton JM (2018) PDBsum: Structural summaries of PDB entries. Prot Sci 27(1):129–134. https://doi.org/10.1002/pro.3289
Longo N, Harding CO, Burton BK, Grange DK, Vockley J, Wasserstein M, Rice GM, Dorenbaum A, Neuenburg JK, Musson DG (2014) Single-dose, subcutaneous recombinant phenylalanine ammonia lyase conjugated with polyethylene glycol in adult patients with phenylketonuria: an open-label, multicentre, phase 1 dose-escalation trial. Lancet 384(9937):37–44. https://doi.org/10.1016/S0140-6736(13)61841-3
Low KO, Mahadi NM, Illias RM (2013) Optimisation of signal peptide for recombinant protein secretion in bacterial hosts. Appl Microbiol Biotechnol 97(9):3811–3826
MacDonald MJ, D’Cunha GB (2007) A modern view of phenylalanine ammonia lyase. Biochem Cell Biol 85(3):273–282. https://doi.org/10.1139/O07-018
Mergulhao F, Summers DK, Monteiro GA (2005) Recombinant protein secretion in Escherichia coli. Biotechnol Adv 23(3):177–202. https://doi.org/10.1016/j.biotechadv.2004.11.003
Nesmeyanova MA, Karamyshev AL, Karamysheva ZN, Kalinin AE, Ksenzenko VN, Kajava AV (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 Lett 403(2):203–207. https://doi.org/10.1016/S0014-5793(97)00052-5
Nielsen H (2017) Predicting secretory proteins with SignalP. Protein Funct Predict Methods Protoc 59–73
Nilsson I, Lara P, Hessa T, Johnson AE, von Heijne G, Karamyshev AL (2015) The code for directing proteins for translocation across ER membrane: SRP cotranslationally recognizes specific features of a signal sequence. J Mol Biol 427(6):1191–1201. https://doi.org/10.1016/j.jmb.2014.06.014
Notredame C, Higgins DG, Heringa J (2000) T-coffee: a novel method for fast and accurate multiple sequence alignment1. J Mol Biol 302(1):205–217. https://doi.org/10.1006/jmbi.2000.4042
Ohmuro-Matsuyama Y, Yamaji H (2017) Modifications of a signal sequence for antibody secretion from insect cells. Cytotechnology 70:1–8. https://doi.org/10.1007/s10616-017-0109-0
Palazzo AF, Springer M, Shibata Y, Lee C-S, Dias AP, Rapoport TA (2007) The signal sequence coding region promotes nuclear export of mRNA. PLoS Biol 5(12):e322. https://doi.org/10.1371/journal.pbio.0050322
Pfeiffer T, Pisch T, Devitt G, Holtkotte D, Bosch V (2006) Effects of signal peptide exchange on HIV-1 glycoprotein expression and viral infectivity in mammalian cells. FEBS Lett 580(15):3775–3778. https://doi.org/10.1016/j.febslet.2006.05.070
Puziss JW, Harvey R, Bassford P (1992) Alterations in the hydrophilic segment of the maltose-binding protein (MBP) signal peptide that affect either export or translation of MBP. J Bacteriol 174(20):6488–6497. https://doi.org/10.1128/jb.174.20.6488-6497.1992
Rapoport TA, Jungnickel B, Kutay U (1996) Protein transport across the eukaryotic endoplasmic reticulum and bacterial inner membranes. Annu Rev Biochem 65(1):271–303. https://doi.org/10.1146/annurev.bi.65.070196.001415
Rusch SL, Chen H, Izard JW, Kendall DA (1994) Signal peptide hydrophobicity is finely tailored for function. J Cell Biochem 55(2):209–217. https://doi.org/10.1002/jcb.240550208
Sakhteman A, Khoddami M, Negahdaripour M, Mehdizadeh A, Tatar M, Ghasemi Y (2016) Exploring 3D structure of human gonadotropin hormone receptor at antagonist state using homology modeling, molecular dynamic simulation, and cross-docking studies. J Mol Model 22(9):225. https://doi.org/10.1007/s00894-016-3091-0
Sarkissian CN, Gámez A (2005) Phenylalanine ammonia lyase, enzyme substitution therapy for phenylketonuria, where are we now?. Mol Genet Metabol 86:22–26. https://doi.org/10.1016/j.ymgme.2005.06.016
Sarkissian CN, Gámez A, Wang L, Charbonneau M, Fitzpatrick P, Lemontt JF, Zhao B, Vellard M, Bell SM, Henschell C (2008) Preclinical evaluation of multiple species of PEGylated recombinant phenylalanine ammonia lyase for the treatment of phenylketonuria. Proc Nat Acad Sci 105(52):20894–20899. https://doi.org/10.1073/pnas.0808421105
Shrivastava A, Khan AA, Khurshid M, Kalam MA, Jain SK, Singhal PK (2016) Recent developments in l-asparaginase discovery and its potential as anticancer agent. Crit Rev Oncol Hematol 100:1–10. https://doi.org/10.1016/j.critrevonc.2015.01.002
Singh P, Sharma L, Kulothungan SR, Adkar BV, Prajapati RS, Ali PSS, Krishnan B, Varadarajan R (2013) Effect of signal peptide on stability and folding of E. coli thioredoxin. PloS one 8(5):e63442. https://doi.org/10.1371/journal.pone.0063442
Sletta H, Tøndervik A, Hakvåg S, Aune TV, Nedal A, Aune R, Evensen G, Valla S, Ellingsen T, Brautaset T (2007) The presence of N-terminal secretion signal sequences leads to strong stimulation of the total expression levels of three tested medically important proteins during high-cell-density cultivations of Escherichia coli. Appl Environ Microbiol 73(3):906–912. https://doi.org/10.1128/AEM.01804-06
Smialowski P, Doose G, Torkler P, Kaufmann S, Frishman D (2012) PROSO II–a new method for protein solubility prediction. FEBS J 279(12):2192–2200. https://doi.org/10.1111/j.1742-4658.2012.08603.x
Sumaily KM, Mujamammi AH (2017) Phenylketonuria: a new look at an old topic, advances in laboratory diagnosis, and therapeutic strategies. Int J Health Sci 11(5):63–70
Turner NJ (2011) Ammonia lyases and aminomutases as biocatalysts for the synthesis of α-amino and β-amino acids. Curr Opin Chem Biol 15(2):234–240. https://doi.org/10.1016/j.cbpa.2010.11.009
von Heijne G (1990) The signal peptide. J Membr Biol 115(3):195–201. https://doi.org/10.1007/BF01868635
Wang C-Z, Chi C-W (2004) Conus peptides—a rich pharmaceutical treasure. Acta Biochim Biophys Sin 36(11):713–723. https://doi.org/10.1093/abbs/36.11.713
Wang L, Gamez A, Archer H, Abola EE, Sarkissian CN, Fitzpatrick P, Wendt D, Zhang Y, Vellard M, Bliesath J (2008) Structural and biochemical characterization of the therapeutic Anabaena variabilis phenylalanine ammonia lyase. J Mol Biol 380(4):623–635. https://doi.org/10.1016/j.jmb.2008.05.025
Watanabe SK, Hernandez-Velazco G, Iturbe-Chinas F, Lopez-Munguia A (1992) Phenylalanine ammonia lyase from Sporidiobolus pararoseus and Rhodosporidium toruloides: Application for phenylalanine and tyrosine deamination. W J Microbiol Biotechnol 8(4):406–410
Waterhouse AM, Procter JB, Martin DM, Clamp M, Barton GJ (2009) Jalview Version 2—a multiple sequence alignment editor and analysis workbench. Bioinformatics 25(9):1189–1191. https://doi.org/10.1093/bioinformatics/btp033
Weltman JK, Skowron G, Loriot GB (2007) Influenza A H5N1 hemagglutinin cleavable signal sequence substitutions. Biochem Biophys Res Commun 352(1):177–180. https://doi.org/10.1016/j.bbrc.2006.10.184
Zalucki YM, Jennings MP (2017) Signal peptidase I processed secretory signal sequences: selection for and against specific amino acids at the second position of mature protein. Biochem Biophys Res Commun 483(3):972–977. https://doi.org/10.1016/j.bbrc.2017.01.044
Zhang W, Xiao W, Wei H, Zhang J, Tian Z (2006) mRNA secondary structure at start AUG codon is a key limiting factor for human protein expression in Escherichia coli. Biochem Biophys Res Commun 349(1):69–78. https://doi.org/10.1016/j.bbrc.2006.07.209
Zhou Y, Lu Z, Wang X, Selvaraj JN, Zhang G (2018) Genetic engineering modification and fermentation optimization for extracellular production of recombinant proteins using Escherichia coli. Appl Microbiol Biotechnol 102(4):1545–1556. https://doi.org/10.1007/s00253-017-8700-z
Zhu F, Liu F, Wu B, He B (2016) Efficient extracellular expression of metalloprotease for Z-aspartame synthesis. J Agric Food Chem 64(51):9631–9638. https://doi.org/10.1021/acs.jafc.6b04164
Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31(13):3406–3415. https://doi.org/10.1093/nar/gkg595
Acknowledgements
Authors would like to thank Shiraz University of Medical Sciences, Shiraz, IRAN for the grant number: 1396-01-36-16684.
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Conflict of interest
The Authors declare that they have no conflict of interest.
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Owji, H., Hemmati, S. A comprehensive in silico characterization of bacterial signal peptides for the excretory production of Anabaena variabilis phenylalanine ammonia lyase in Escherichia coli. 3 Biotech 8, 488 (2018). https://doi.org/10.1007/s13205-018-1517-3
Received:
Accepted:
Published:
DOI: https://doi.org/10.1007/s13205-018-1517-3