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Hashemzaei M, Nezafat N, Ghoshoon MB, Negahdaripour M. In-silico selection of appropriate signal peptides for romiplostim secretory production in Escherichia coli. INFORMATICS IN MEDICINE UNLOCKED 2022. [DOI: 10.1016/j.imu.2022.101146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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2
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Lorrine OE, Raja Abd. Rahman RNZ, Tan JS, Raja Khairuddin RF, Salleh AB, Oslan SN. Determination of Putative Vacuolar Proteases, PEP4 and PRB1 in a Novel Yeast Expression Host Meyerozyma guilliermondii Strain SO Using Bioinformatics Tools. PERTANIKA JOURNAL OF SCIENCE AND TECHNOLOGY 2022. [DOI: 10.47836/pjst.30.1.42] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Meyerozyma guilliermondii strain SO, a newly isolated yeast species from spoilt orange, has been used as a host to express the recombinant proteins using methylotrophic yeast promoters. However, as a novel yeast expression system, the vacuolar proteases of this yeast have not been determined, which may have contributed to the low level of heterologous protein secretions. Thus, this study aimed to determine intra- and extracellular proteolytic activity and identify the putative vacuolar proteases using bioinformatics techniques. A clear zone was observed from the nutrient agar skimmed milk screening plate. Proteolytic activity of 117.30 U/ml and 75 U/ml were obtained after 72 h of cultivation for both extracellular and intracellular proteins, respectively. Next, the Hidden Markov model (HMM) was used to detect the presence of the vacuolar proteases (PEP4 and PRB1) from the strain SO proteome. Aspartyl protease (PEP4) with 97.55% identity to Meyerozyma sp. JA9 and a serine protease (PRB1) with 70.91% identity to Candida albicans were revealed. The homology with other yeast vacuolar proteases was confirmed via evolutionary analysis. PROSPER tool prediction of cleavage sites postulated that PEP4 and PRB1 might have caused proteolysis of heterologous proteins in strain SO. In conclusion, two putative vacuolar proteases (PEP4 and PRB1) were successfully identified in strain SO. Further characterization can be done to understand their specific properties, and their effects on heterologous protein expression can be conducted via genome editing.
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Vakili O, Khatami SH, Maleksabet A, Movahedpour A, Fana SE, Sadegh R, Salmanzadeh AH, Razeghifam H, Nourdideh S, Tehrani SS, Taheri-Anganeh M. Finding Appropriate Signal Peptides for Secretory Production of Recombinant Glucarpidase: An In SilicoMethod. Recent Pat Biotechnol 2021; 15:302-315. [PMID: 34547999 DOI: 10.2174/1872208315666210921095420] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 06/16/2021] [Accepted: 08/02/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Methotrexate (MTX) is a general chemotherapeutic agent utilized to treat a variety of malignancies, woefully, its high doses can cause nephrotoxicity and subsequent defect in the process of MTX excretion. The recombinant form of glucarpidase is produced by engineered E. coli and is a confirmed choice to overcoming this problem. OBJECTIVE In the present study, in silico analyses were performed to select suitable SPs for the secretion of recombinant glucarpidase in E. coli. METHODS The signal peptide website and UniProt database were employed to collect the SPs and protein sequences. In the next step, SignalP-5.0 helped us to predict the SPs and the position of cleavage sites. Moreover, physicochemical properties and solubility were evaluated using Prot- Param and Protein-sol online software, and finally, ProtCompB was used to predict the final subcellular localization. RESULTS Luckily, all SPs could form soluble fusion proteins. At last, it was found that PPB and TIBA could translocate the glucarpidase into the extracellular compartment. CONCLUSION This study showed that there are only 2 applicable SPs for the extracellular translocation of glucarpidase. Although the findings were remarkable with high degrees of accuracy and precision based on the utilization of bioinformatics analyses, additional experimental assessments are required to confirm and validate it. Recent patents revealed several inventions related to the clinical aspects of vaccine peptides against human disorders.
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Affiliation(s)
- Omid Vakili
- Department of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Seyyed Hossein Khatami
- Department of Clinical Biochemistry, School of Medicine, Shahid Beheshti University of Medical Science, Tehran, Iran
| | - Amir Maleksabet
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Ahmad Movahedpour
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Saeed Ebrahimi Fana
- Department of Clinical Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | | | | | | | | | - Sadra Samavarchi Tehrani
- Department of Clinical Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mortaza Taheri-Anganeh
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
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Bhandari BK, Lim CS, Gardner PP. TISIGNER.com: web services for improving recombinant protein production. Nucleic Acids Res 2021; 49:W654-W661. [PMID: 33744969 PMCID: PMC8265118 DOI: 10.1093/nar/gkab175] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/17/2021] [Accepted: 03/03/2021] [Indexed: 12/25/2022] Open
Abstract
Experiments that are planned using accurate prediction algorithms will mitigate failures in recombinant protein production. We have developed TISIGNER (https://tisigner.com) with the aim of addressing technical challenges to recombinant protein production. We offer three web services, TIsigner (Translation Initiation coding region designer), SoDoPE (Soluble Domain for Protein Expression) and Razor, which are specialised in synonymous optimisation of recombinant protein expression, solubility and signal peptide analysis, respectively. Importantly, TIsigner, SoDoPE and Razor are linked, which allows users to switch between the tools when optimising genes of interest.
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Affiliation(s)
- Bikash K Bhandari
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand
| | - Chun Shen Lim
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand
| | - Paul P Gardner
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand
- Biomolecular Interaction Centre, University of Canterbury, Christchurch 8140, New Zealand
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Comparison of Different Signal Sequences to Use for Periplasmic Over-Expression of Buforin I in Escherichia coli: An In Silico Study. Int J Pept Res Ther 2020. [DOI: 10.1007/s10989-020-10042-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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6
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In Silico Study of Different Signal Peptides to Express Recombinant Glutamate Decarboxylase in the Outer Membrane of Escherichia coli. Int J Pept Res Ther 2019. [DOI: 10.1007/s10989-019-09986-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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7
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Experimental Evaluation of In Silico Selected Signal Peptides for Secretory Expression of Erwinia Asparaginase in Escherichia coli. Int J Pept Res Ther 2019. [DOI: 10.1007/s10989-019-09961-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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8
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Vasiee A, Norouzi N, Yazdi FT, Mortazavi SA, Sankian M, Mahmoudi M, Shahidi F. Analysis of different signal peptides for the secretory production of Ama r 2 in gram-positive systems (Lactococcus lactis). Microb Pathog 2019; 138:103819. [PMID: 31669829 DOI: 10.1016/j.micpath.2019.103819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 10/22/2019] [Accepted: 10/23/2019] [Indexed: 11/19/2022]
Abstract
Prokaryotic systems have been considered the most affordable and simplest hosts which are being employed to express recombinant proteins such as allergens; nevertheless, without appropriate signal peptide (SP), these systems cannot be used for secretory proteins. Recently, a lot of effort has been put into assessing the potential of gram-positive strains such as lactic acid bacteria for new applications in the production of heterologous proteins. Ama r 2 is a respiratory allergen from Amaranthus retroflexus, whose recombinant production in the probiotic host could be introduced as a specific and effective way to rapid diagnosis and immunotherapy of this allergy. Consequently, the production of this recombinant protein using the prokaryotic system, requires a suitable SP to protect disulfide bonds and to prevent misfolding. This study was designed to predict the best SPs for the expression of Ama r 2 protein in Lactococcus lactis as the host. In this study, 42 signal sequences were selected from SP databases and the most important features of them were evaluated. First, n, h and c regions of the SPs and their probabilities were investigated by signalP software version 4.1. Then, their physicochemical properties were evaluated by Portparam and SOLpro. Moreover, the secretion sorting and sub-cellular localization sites were evaluated by PRED-TAT and ProtcompB software programs. The results revealed that yjgB, entC2 (Entrotoxine type C-2), ent B (Entrotoxine type), blaZ (Beta lactamase), dex (number 21), blm (Beta lactamase 2), dex (Dextranase; number 20) and number 26 were introduced theatrically as the best SPs to express Ama r 2 in Lactococcus lactis.
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Affiliation(s)
- Alireza Vasiee
- Department of Food Science and Technology, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Neda Norouzi
- University Medical Center Groningen, Antonius Deusinglaan 1, 9713, AV, the Netherlands
| | - Farideh Tabatabaee Yazdi
- Department of Food Science and Technology, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Seyed Ali Mortazavi
- Department of Food Science and Technology, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran.
| | - Mojtaba Sankian
- Immunology Research Center, Bu-Ali Research Institute, School of Medicine, University of Medical Sciences, Mashhad, Iran
| | - Mahmoud Mahmoudi
- Immunology Research Center, Bu-Ali Research Institute, School of Medicine, University of Medical Sciences, Mashhad, Iran
| | - Fakhri Shahidi
- Department of Food Science and Technology, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
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In silico analysis of different signal peptides for the secretory production of recombinant human keratinocyte growth factor in Escherichia coli. Comput Biol Chem 2019; 80:225-233. [DOI: 10.1016/j.compbiolchem.2019.03.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Revised: 01/23/2019] [Accepted: 03/11/2019] [Indexed: 12/31/2022]
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10
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Nazifi N, Tahmoorespur M, Sekhavati MH, Haghparast A, Behroozikhah MA. Assessment of Signal Peptides to Optimize Interleukin 2 (IL-2) Folding and Expression. CURR PROTEOMICS 2019. [DOI: 10.2174/1570164615666181024113612] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:Using a bacterial expression system such as Escherichia coli (E. coli) is very common for protein expression because of its simplicity, low cost and high efficiency.Objective:In order to express proteins that contain di-sulfide bands, an oxidative space such as the periplasmic environment of the bacteria is required. Therefore, a leader sequence which named Signal Peptide (SP) is needed to direct recombinant protein to fold in periplasmic space. Interleukin-2 (IL-2) is a prominent cytokine which known as growth factor for T-cells and typically produced by a variety of immune cells that stimulate and regulate inflammatory and immune responses.Methods:This study was designed to predict the best signal peptides to express IL-2 in E. coli. To predict the best signal peptides for the expression of IL-2 in Gram-negative bacteria (E. coli), forty-five sequences of SPs were extracted from data base. Some most important details such as n, h and c regions of signal peptides and their probability were studied through the signalP software. </P><P> Afterwards, physico–chemical features of SPs were analyzed by Portparam and Solpro tools. Finally, secretion-pathway and sub-cellular localization sites were evaluated by PRED-TAT and ProtcompB softwares.Results:At the end of the in-silico analyzes, it was determined that ccmH, PelB, traU, yohN, lolA, yhcN are the most reliable SPs, respectively, with highest score and best performing to express the IL-2 protein in E. coli.
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Affiliation(s)
- Narges Nazifi
- Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Mojtaba Tahmoorespur
- Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Mohammad Hadi Sekhavati
- Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Alireza Haghparast
- Pathobiology Department, School of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Mohammad Ali Behroozikhah
- Department of Brucellosis, Razi Vaccine and Serum Research Institute, Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran
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In silico Analysis of Different Signal Peptides for the Excretory Production of Recombinant NS3-GP96 Fusion Protein in Escherichia coli. Int J Pept Res Ther 2018. [DOI: 10.1007/s10989-018-9775-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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12
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Darvishi F, Zarei A, Madzak C. In silico and in vivo analysis of signal peptides effect on recombinant glucose oxidase production in nonconventional yeast Yarrowia lipolytica. World J Microbiol Biotechnol 2018; 34:128. [PMID: 30083963 DOI: 10.1007/s11274-018-2512-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Accepted: 07/31/2018] [Indexed: 11/26/2022]
Abstract
Signal peptide (SP) is an important factor and biobrick in the production and secretion of recombinant proteins. The aim of this study was in silico and in vivo analysis of SPs effect on the production of recombinant glucose oxidase (GOX) in Yarrowia lipolytica. Several in silico softwares, namely SignalP4, Signal-CF, Phobius, WolfPsort 0.2, SOLpro and ProtParam, were used to analyse the potential of 15 endogenous and exogenous SPs for the secretion of recombinant GOX in Y. lipolytica. According to in silico results, the SP of GOX was predicted as suitable in terms of high secretory potential and of protein solubility and stability which is chosen for in vivo analysis. The recombinant Y. lipolytica strain produced 280 U/L of extracellular GOX after 7 days in YPD medium. The results show that the SP of GOX can be applied to efficient production of extracellular heterologous proteins and metabolic engineering in Y. lipolytica.
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Affiliation(s)
- Farshad Darvishi
- Microbial Biotechnology and Bioprocess Engineering (MBBE) Group, Department of Microbiology, Faculty of Science, University of Maragheh, Maragheh, 55181-83111, Iran.
| | - Amin Zarei
- Microbial Biotechnology and Bioprocess Engineering (MBBE) Group, Department of Microbiology, Faculty of Science, University of Maragheh, Maragheh, 55181-83111, Iran
| | - Catherine Madzak
- UMR GMPA, AgroParisTech, INRA, Université Paris-Saclay, Thiverval-Grignon, France
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13
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A comprehensive review of signal peptides: Structure, roles, and applications. Eur J Cell Biol 2018; 97:422-441. [DOI: 10.1016/j.ejcb.2018.06.003] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 06/18/2018] [Accepted: 06/18/2018] [Indexed: 01/06/2023] Open
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14
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Optimization of Human Serum Albumin Periplasmic Localization in Escherichia coli Using In Silico Evaluation of Different Signal Peptides. Int J Pept Res Ther 2018. [DOI: 10.1007/s10989-018-9709-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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15
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In Silico B Cell and T Cell Epitopes Evaluation of lipL32 and OmpL1 Proteins for Designing a Recombinant Multi-Epitope Vaccine Against Leptospirosis. ACTA ACUST UNITED AC 2018. [DOI: 10.5812/iji.63255] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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16
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Bagherinejad MR, Sadeghi HMM, Abedi D, Moazen F, Rabbani M. Effect of Twine-arginine Translocation-signaling Fusion System and Chaperones Co-expression on Secretory Expression of Somatropin. Adv Biomed Res 2018; 7:17. [PMID: 29456988 PMCID: PMC5812091 DOI: 10.4103/abr.abr_273_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Background: Twine-arginine translocation (TAT) system is one of the exporting systems in Escherichia coli which could transport fully/semi-correctly folded proteins outside the reductive cytoplasmic space. In combination with co-expression with a chaperone system, the correctly folded proteins could be transported to oxidative periplasmic space and culture media to pass the main limitations in E. coli expression system such as misfolding and inclusion body formation. Materials and Methods: To study the effectiveness of signaling sequences and chaperone co-expression on the translocation of expressed protein, somatropin was selected as the target. Two common signal sequences in TAT system (TorA and SufI) were added at the N-terminal of somatropin and the cassettes were co-expressed in E. coli BL21 (DE3) by a chaperone team including DnaK/J-GrpeE. Results: The expression pattern studies including Western blotting and sodium dodecyl sulfate polyacrylamide gel electrophoresis confirmed that somatropin is expressed in two cassettes. However, the pattern was different for two signaling sequences. Conclusion: The results confirmed that the approach of using TAT-signaling sequences and co-expression with the chaperone team could enhance translocation of protein to periplasmic space and culture media compared to control groups. Western blotting results showed that the signal sequence TorA could transport more expressed proteins to the periplasmic space and culture media in comparison with SufI. However, there was a considerable amount of human growth hormone in the cytoplasm which could not be transported outside the cytoplasmic space.
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Affiliation(s)
- Mohammad Reza Bagherinejad
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Hamid Mir-Mohammad Sadeghi
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Daryoush Abedi
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Fateme Moazen
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mohammad Rabbani
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Isfahan University of Medical Sciences, Isfahan, Iran
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Investigating CRISPR-Cas systems in Clostridium botulinum via bioinformatics tools. INFECTION GENETICS AND EVOLUTION 2017; 54:355-373. [DOI: 10.1016/j.meegid.2017.06.027] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 06/19/2017] [Accepted: 06/27/2017] [Indexed: 12/22/2022]
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18
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Ling HL, Rahmat Z, Murad AMA, Mahadi NM, Illias RM. Proteome-based identification of signal peptides for improved secretion of recombinant cyclomaltodextrin glucanotransferase in Escherichia coli. Process Biochem 2017. [DOI: 10.1016/j.procbio.2017.06.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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19
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Negahdaripour M, Golkar N, Hajighahramani N, Kianpour S, Nezafat N, Ghasemi Y. Harnessing self-assembled peptide nanoparticles in epitope vaccine design. Biotechnol Adv 2017; 35:575-596. [PMID: 28522213 PMCID: PMC7127164 DOI: 10.1016/j.biotechadv.2017.05.002] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 04/23/2017] [Accepted: 05/11/2017] [Indexed: 12/11/2022]
Abstract
Vaccination has been one of the most successful breakthroughs in medical history. In recent years, epitope-based subunit vaccines have been introduced as a safer alternative to traditional vaccines. However, they suffer from limited immunogenicity. Nanotechnology has shown value in solving this issue. Different kinds of nanovaccines have been employed, among which virus-like nanoparticles (VLPs) and self-assembled peptide nanoparticles (SAPNs) seem very promising. Recently, SAPNs have attracted special interest due to their unique properties, including molecular specificity, biodegradability, and biocompatibility. They also resemble pathogens in terms of their size. Their multivalency allows an orderly repetitive display of antigens on their surface, which induces a stronger immune response than single immunogens. In vaccine design, SAPN self-adjuvanticity is regarded an outstanding advantage, since the use of toxic adjuvants is no longer required. SAPNs are usually composed of helical or β-sheet secondary structures and are tailored from natural peptides or de novo structures. Flexibility in subunit selection opens the door to a wide variety of molecules with different characteristics. SAPN engineering is an emerging area, and more novel structures are expected to be generated in the future, particularly with the rapid progress in related computational tools. The aim of this review is to provide a state-of-the-art overview of self-assembled peptide nanoparticles and their use in vaccine design in recent studies. Additionally, principles for their design and the application of computational approaches to vaccine design are summarized.
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Affiliation(s)
- Manica Negahdaripour
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran; Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Nasim Golkar
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran; Pharmaceutics Department, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Nasim Hajighahramani
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran; Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Sedigheh Kianpour
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran; Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Navid Nezafat
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Younes Ghasemi
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran; Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran; Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran; Biotechnology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
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Assessment of Prokaryotic Signal Peptides for Secretion of Tumor Necrosis Factor Related Apoptosis Inducing Ligand (TRAIL) in E. coli: An in silico Approach. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2016. [DOI: 10.22207/jpam.10.4.22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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21
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Rahmatabadi SS, Nezafat N, Negahdaripour M, Hajighahramani N, Morowvat MH, Ghasemi Y. Studying the features of 57 confirmed CRISPR loci in 29 strains of Escherichia coli. J Basic Microbiol 2016; 56:645-53. [PMID: 26871258 DOI: 10.1002/jobm.201500707] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 01/17/2016] [Indexed: 12/26/2022]
Abstract
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) system is a novel type of innate defense system in prokaryotes for destruction of exogenous elements. To gain further insight into behavior and organization of the system, the extensive analysis of the available sequenced genomes is necessary. The dynamic nature of CRISPR loci is possibly valuable for typing and relative analyses of strains and microbial population. There are a few orderly bioinformatics investigations about the structure of CRISPR sequences in the Escherichia coli strains. In this study, 57 CRISPR loci were selected from 32 Escherichia coli strains to investigate their structural characteristics and potential functions using bioinformatics tools. Our results showed that most strains contained several loci that mainly included conserved direct repeats, while the spacers were highly variable. Moreover, RNA analysis of the sequences indicated that all loci could form stable RNA secondary structures and showed homology mostly with phages compared to plasmids. Only three strains included cas genes around their loci.
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Affiliation(s)
- Seyyed Soheil Rahmatabadi
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran.,Pharmaceutical Science Research Center, Shiraz University of Medical Science, Shiraz, Iran
| | - Navid Nezafat
- Pharmaceutical Science Research Center, Shiraz University of Medical Science, Shiraz, Iran
| | - Manica Negahdaripour
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran.,Pharmaceutical Science Research Center, Shiraz University of Medical Science, Shiraz, Iran
| | - Nasim Hajighahramani
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran.,Pharmaceutical Science Research Center, Shiraz University of Medical Science, Shiraz, Iran
| | | | - Younes Ghasemi
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran.,Pharmaceutical Science Research Center, Shiraz University of Medical Science, Shiraz, Iran.,Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
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22
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Bagherinejad MR, Sadeghi HMM, Abedi D, Chou CP, Moazen F, Rabbani M. Twin arginine translocation system in secretory expression of recombinant human growth hormone. Res Pharm Sci 2016; 11:461-469. [PMID: 28003839 PMCID: PMC5168882 DOI: 10.4103/1735-5362.194871] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Recombinant protein production in E. coli has several advantages over other expression systems. Misfolding, inclusion body formation, and lack of eukaryotic post translational modification are the most disadvantages of this system. Exporting of correctly folded proteins to the outside of reductive cytoplasmic environment through twin-arginine system could help to pass these limiting steps. Two signal sequences, TorA and SufI are used at N-terminal of human growth hormone (hGH) bearing DsbA gene sequence at C-terminal to enhance folding. The synthetic cassettes including the signal sequence, hGH and DsbA were transformed into E. coli BL21 (DE3) to study the effect of signal sequence and DsbA chaperone on translocation and folding of the protein. The results confirmed using signal sequence at N-terminal of targeted protein and coexpression with DsbA could transport proteins to the periplasmic space and culture media compared to control groups. Although there is no protein band of somatropin in SDS-Page of culture media samples when using SufI as signaling sequence, the study demonstrated TorA signal sequence could transport the target protein to the culture media. However, there was a considerable amount of hGH in periplasmic space when using SufI compared to control.
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Affiliation(s)
- Mohammad Reza Bagherinejad
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Isfahan University of Medical Sciences, Isfahan, I.R. Iran
| | - Hamid Mir-Mohammad Sadeghi
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Isfahan University of Medical Sciences, Isfahan, I.R. Iran
| | - Daryoush Abedi
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Isfahan University of Medical Sciences, Isfahan, I.R. Iran
| | - C Perry Chou
- Department of Chemical Engineering, University of Waterloo, Waterloo, Ontario, Canada
| | - Fatemeh Moazen
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Isfahan University of Medical Sciences, Isfahan, I.R. Iran
| | - Mohammad Rabbani
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Isfahan University of Medical Sciences, Isfahan, I.R. Iran
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Durrani FG, Gul R, Sadaf S, Akhtar MW. Expression and rapid purification of recombinant biologically active ovine growth hormone with DsbA targeting to Escherichia coli inner membrane. Appl Microbiol Biotechnol 2015; 99:6791-801. [DOI: 10.1007/s00253-015-6751-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Revised: 05/20/2015] [Accepted: 06/04/2015] [Indexed: 11/29/2022]
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Cloning, Characterization and Bioinformatics Analysis of Novel Cytosine Deaminase from Escherichia coli AGH09. Int J Pept Res Ther 2015. [DOI: 10.1007/s10989-015-9465-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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