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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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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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3
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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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4
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Hansen KG, Boos F, Herrmann JM. Accessory signals in protein translocation. Aging (Albany NY) 2018; 10:530-531. [PMID: 29706613 PMCID: PMC5940120 DOI: 10.18632/aging.101435] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 04/27/2018] [Indexed: 12/04/2022]
Affiliation(s)
- Katja G. Hansen
- Cell Biology, University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Felix Boos
- Cell Biology, University of Kaiserslautern, 67663 Kaiserslautern, Germany
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Kaberniuk AA, Morano NC, Verkhusha VV, Snapp EL. moxDendra2: an inert photoswitchable protein for oxidizing environments. Chem Commun (Camb) 2018; 53:2106-2109. [PMID: 28133646 DOI: 10.1039/c6cc09997a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Fluorescent proteins (FPs) that can be optically highlighted enable PALM super-resolution microscopy and pulse-chase experiments of cellular molecules. Most FPs evolved in cytoplasmic environments either in the original source organism or in the cytoplasm of bacteria during the course of optimization for research applications. Consequently, many FPs may fold incorrectly in the chemically distinct environments in subcellular organelles. Here, we describe the first monomeric photoswitchable (from green to bright red) FP adapted for oxidizing environments.
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Affiliation(s)
- Andrii A Kaberniuk
- Albert Einstein College of Medicine, Department of Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Nicholas C Morano
- Albert Einstein College of Medicine, Department of Biochemistry, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Vladislav V Verkhusha
- Albert Einstein College of Medicine, Department of Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Erik Lee Snapp
- Janelia Research Campus, HHMI, 19700 Helix Drive, Ashburn, VA 20147, USA.
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Han S, Machhi S, Berge M, Xi G, Linke T, Schoner R. Novel signal peptides improve the secretion of recombinant Staphylococcus aureus Alpha toxin H35L in Escherichia coli. AMB Express 2017; 7:93. [PMID: 28497288 PMCID: PMC5427057 DOI: 10.1186/s13568-017-0394-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Accepted: 04/26/2017] [Indexed: 11/10/2022] Open
Abstract
Secretion of heterologous proteins into Escherichia coli cell culture medium offers significant advantages for downstream processing over production as inclusion bodies; including cost and time savings, and reduction of endotoxin. Signal peptides play an important role in targeting proteins for translocation across the cytoplasmic membrane to the periplasmic space and release into culture medium during the secretion process. Alpha toxinH35L (ATH35L) was selected as an antigen for vaccine development against Staphylococcus aureus infections. It was successfully secreted into culture medium of E. coli by using bacterial signal peptides linked to the N-terminus of the protein. In order to improve the level of secreted ATH35L, we designed a series of novel signal peptides by swapping individual domains of modifying dsbA and pelB signal peptides and tested them in a fed-batch fermentation process. The data showed that some of the modified signal peptides improved the secretion efficiency of ATH35L compared with E. coli signal peptides from dsbA, pelB and phoA proteins. Indeed, one of the novel signal peptides improved the yield of secreted ATH35L by 3.5-fold in a fed-batch fermentation process and at the same time maintained processing at the expected site for signal peptide cleavage. Potentially, these new novel signal peptides can be used to improve the secretion efficiency of other heterologous proteins in E. coli. Furthermore, analysis of the synthetic signal peptide amino acid sequences provides some insight into the sequence features within the signal peptide that influence secretion efficiency.
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Orfanoudaki G, Markaki M, Chatzi K, Tsamardinos I, Economou A. MatureP: prediction of secreted proteins with exclusive information from their mature regions. Sci Rep 2017; 7:3263. [PMID: 28607462 PMCID: PMC5468347 DOI: 10.1038/s41598-017-03557-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 04/28/2017] [Indexed: 11/09/2022] Open
Abstract
More than a third of the cellular proteome is non-cytoplasmic. Most secretory proteins use the Sec system for export and are targeted to membranes using signal peptides and mature domains. To specifically analyze bacterial mature domain features, we developed MatureP, a classifier that predicts secretory sequences through features exclusively computed from their mature domains. MatureP was trained using Just Add Data Bio, an automated machine learning tool. Mature domains are predicted efficiently with ~92% success, as measured by the Area Under the Receiver Operating Characteristic Curve (AUC). Predictions were validated using experimental datasets of mutated secretory proteins. The features selected by MatureP reveal prominent differences in amino acid content between secreted and cytoplasmic proteins. Amino-terminal mature domain sequences have enhanced disorder, more hydroxyl and polar residues and less hydrophobics. Cytoplasmic proteins have prominent amino-terminal hydrophobic stretches and charged regions downstream. Presumably, secretory mature domains comprise a distinct protein class. They balance properties that promote the necessary flexibility required for the maintenance of non-folded states during targeting and secretion with the ability of post-secretion folding. These findings provide novel insight in protein trafficking, sorting and folding mechanisms and may benefit protein secretion biotechnology.
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Affiliation(s)
- Georgia Orfanoudaki
- Institute of Molecular Biology and Biotechnology-FORTH and Department of Biology-University of Crete, PO Box 1385, Heraklion, Crete, Greece
| | - Maria Markaki
- Computer Science Department, University of Crete, Heraklion, Greece
| | - Katerina Chatzi
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, B-3000, Leuven, Belgium
| | - Ioannis Tsamardinos
- Computer Science Department, University of Crete, Heraklion, Greece.,Gnosis Data Analysis PC, Heraklion, Greece
| | - Anastassios Economou
- Institute of Molecular Biology and Biotechnology-FORTH and Department of Biology-University of Crete, PO Box 1385, Heraklion, Crete, Greece. .,KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, B-3000, Leuven, Belgium.
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Bienvenut WV, Giglione C, Meinnel T. Proteome-wide analysis of the amino terminal status of Escherichia coli proteins at the steady-state and upon deformylation inhibition. Proteomics 2016; 15:2503-18. [PMID: 26017780 DOI: 10.1002/pmic.201500027] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 05/18/2015] [Accepted: 05/21/2015] [Indexed: 12/14/2022]
Abstract
A proteome wide analysis was performed in Escherichia coli to identify the impact on protein N-termini of actinonin, an antibiotic specifically inhibiting peptide deformylase (PDF). A strategy and tool suite (SILProNaQ) was employed to provide large-scale quantitation of N-terminal modifications. In control conditions, more than 1000 unique N-termini were identified with 56% showing initiator methionine removal. Additional modifications corresponded to partial or complete Nα-acetylation (10%) and N-formyl retention (5%). Among the proteins undergoing these N-terminal modifications, 140 unique N-termini from translocated membrane proteins were highlighted. The very early time-course impact of actinonin was followed after addition of bacteriostatic concentrations of the drug. Under these conditions, 26% of all proteins did not undergo deformylation any longer after 10 min, a value reaching more than 60% of all characterized proteins after 40 min of treatment. The N-formylation ratio measured on individual proteins increased with the same trend. Upon early PDF inhibition, two major categories of proteins retained their N-formyl group: a large number of inner membrane proteins and many proteins involved in protein synthesis including factors assisting the nascent chains in early cotranslational events. All MS data have been deposited in the ProteomeXchange with identifiers PXD001979, PXD002012 and PXD001983 (http://proteomecentral.proteomexchange.org/dataset/PXD001979, http://proteomecentral.proteomexchange.org/dataset/PXD002012 and http://proteomecentral.proteomexchange.org/dataset/PXD001983).
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Affiliation(s)
- Willy V Bienvenut
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Gif-sur-Yvette, France
| | - Carmela Giglione
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Gif-sur-Yvette, France
| | - Thierry Meinnel
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Gif-sur-Yvette, France
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Orfanoudaki G, Economou A. Proteome-wide subcellular topologies of E. coli polypeptides database (STEPdb). Mol Cell Proteomics 2014; 13:3674-87. [PMID: 25210196 DOI: 10.1074/mcp.o114.041137] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Cell compartmentalization serves both the isolation and the specialization of cell functions. After synthesis in the cytoplasm, over a third of all proteins are targeted to other subcellular compartments. Knowing how proteins are distributed within the cell and how they interact is a prerequisite for understanding it as a whole. Surface and secreted proteins are important pathogenicity determinants. Here we present the STEP database (STEPdb) that contains a comprehensive characterization of subcellular localization and topology of the complete proteome of Escherichia coli. Two widely used E. coli proteomes (K-12 and BL21) are presented organized into thirteen subcellular classes. STEPdb exploits the wealth of genetic, proteomic, biochemical, and functional information on protein localization, secretion, and targeting in E. coli, one of the best understood model organisms. Subcellular annotations were derived from a combination of bioinformatics prediction, proteomic, biochemical, functional, topological data and extensive literature re-examination that were refined through manual curation. Strong experimental support for the location of 1553 out of 4303 proteins was based on 426 articles and some experimental indications for another 526. Annotations were provided for another 320 proteins based on firm bioinformatic predictions. STEPdb is the first database that contains an extensive set of peripheral IM proteins (PIM proteins) and includes their graphical visualization into complexes, cellular functions, and interactions. It also summarizes all currently known protein export machineries of E. coli K-12 and pairs them, where available, with the secretory proteins that use them. It catalogs the Sec- and TAT-utilizing secretomes and summarizes their topological features such as signal peptides and transmembrane regions, transmembrane topologies and orientations. It also catalogs physicochemical and structural features that influence topology such as abundance, solubility, disorder, heat resistance, and structural domain families. Finally, STEPdb incorporates prediction tools for topology (TMHMM, SignalP, and Phobius) and disorder (IUPred) and implements the BLAST2STEP that performs protein homology searches against the STEPdb.
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Affiliation(s)
- Georgia Orfanoudaki
- From the ‡Institute of Molecular Biology and Biotechnology-FoRTH and §Department of Biology-University of Crete, P.O. Box 1385, Iraklio, Crete, Greece
| | - Anastassios Economou
- From the ‡Institute of Molecular Biology and Biotechnology-FoRTH and §Department of Biology-University of Crete, P.O. Box 1385, Iraklio, Crete, Greece; ¶Laboratory of Molecular Bacteriology; Rega Institute, Department of Microbiology and Immunology, KU Leuven, Herrestraat 49, B-3000 Leuven, Belgium
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Low KO, Muhammad Mahadi N, Md. Illias R. Optimisation of signal peptide for recombinant protein secretion in bacterial hosts. Appl Microbiol Biotechnol 2013; 97:3811-26. [DOI: 10.1007/s00253-013-4831-z] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2013] [Revised: 03/03/2013] [Accepted: 03/04/2013] [Indexed: 10/27/2022]
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Mechanistic link between β barrel assembly and the initiation of autotransporter secretion. Proc Natl Acad Sci U S A 2013; 110:E938-47. [PMID: 23431155 DOI: 10.1073/pnas.1219076110] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Autotransporters are bacterial virulence factors that contain an N-terminal extracellular ("passenger") domain and a C-terminal β barrel ("β") domain that anchors the protein to the outer membrane. The β domain is required for passenger domain secretion, but its exact role in autotransporter biogenesis is unclear. Here we describe insights into the function of the β domain that emerged from an analysis of mutations in the Escherichia coli O157:H7 autotransporter EspP. We found that the G1066A and G1081D mutations slightly distort the structure of the β domain and delay the initiation of passenger domain translocation. Site-specific photocrosslinking experiments revealed that the mutations slow the insertion of the β domain into the outer membrane, but do not delay the binding of the β domain to the factor that mediates the insertion reaction (the Bam complex). Our results demonstrate that the β domain does not simply target the passenger domain to the outer membrane, but promotes translocation when it reaches a specific stage of assembly. Furthermore, our results provide evidence that the Bam complex catalyzes the membrane integration of β barrel proteins in a multistep process that can be perturbed by minor structural defects in client proteins.
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Liu S, Zhang D, Wang M, Cui W, Chen K, Liu Y, Du G, Chen J, Zhou Z. The pro-region of Streptomyces hygroscopicus transglutaminase affects its secretion by Escherichia coli. FEMS Microbiol Lett 2011; 324:98-105. [DOI: 10.1111/j.1574-6968.2011.02387.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2011] [Revised: 07/23/2011] [Accepted: 08/10/2011] [Indexed: 11/30/2022] Open
Affiliation(s)
- Song Liu
- Key Laboratory of Industrial Biotechnology; Ministry of Education; School of Biotechnology; Jiangnan University; Wuxi; China
| | - Dongxu Zhang
- Key Laboratory of Industrial Biotechnology; Ministry of Education; School of Biotechnology; Jiangnan University; Wuxi; China
| | | | - Wenjing Cui
- Key Laboratory of Industrial Biotechnology; Ministry of Education; School of Biotechnology; Jiangnan University; Wuxi; China
| | - Kangkang Chen
- Key Laboratory of Industrial Biotechnology; Ministry of Education; School of Biotechnology; Jiangnan University; Wuxi; China
| | - Yi Liu
- Key Laboratory of Industrial Biotechnology; Ministry of Education; School of Biotechnology; Jiangnan University; Wuxi; China
| | - Guocheng Du
- Key Laboratory of Industrial Biotechnology; Ministry of Education; School of Biotechnology; Jiangnan University; Wuxi; China
| | | | - Zhemin Zhou
- Key Laboratory of Industrial Biotechnology; Ministry of Education; School of Biotechnology; Jiangnan University; Wuxi; China
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Aronson DE, Costantini LM, Snapp EL. Superfolder GFP is fluorescent in oxidizing environments when targeted via the Sec translocon. Traffic 2011; 12:543-8. [PMID: 21255213 DOI: 10.1111/j.1600-0854.2011.01168.x] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The ability to study proteins in live cells using genetically encoded fluorescent proteins (FPs) has revolutionized cell biology (1-3). Researchers have created numerous FP biosensors and optimized FPs for specific organisms and subcellular environments in a rainbow of colors (4,5). However, expressing FPs in oxidizing environments such as the eukaryotic endoplasmic reticulum (ER) or the bacterial periplasm can impair folding, thereby preventing fluorescence (6,7). A substantial fraction of enhanced green fluorescent protein (EGFP) oligomerizes to form non-fluorescent mixed disulfides in the ER (6) and EGFP does not fluoresce in the periplasm when targeted via the SecYEG translocon (7). To overcome these obstacles, we exploited the highly efficient folding capability of superfolder GFP (sfGFP) (8). Here, we report sfGFP does not form disulfide-linked oligomers in the ER and maltose-binding protein (MBP) signal sequence (peri)-sfGFP (9) is brightly fluorescent in the periplasm of Escherichia coli. Thus, sfGFP represents an important research tool for studying resident proteins of oxidizing environments.
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Affiliation(s)
- Deborah E Aronson
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
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Detecting folding intermediates of a protein as it passes through the bacterial translocation channel. Cell 2009; 138:1164-73. [PMID: 19766568 DOI: 10.1016/j.cell.2009.07.030] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2009] [Revised: 05/04/2009] [Accepted: 07/16/2009] [Indexed: 11/20/2022]
Abstract
Most bacterial exported proteins cross the cytoplasmic membrane as unfolded polypeptides. However, little is known about how they fold during or after this process due to the difficulty in detecting folding intermediates. Here we identify cotranslational and posttranslational folding intermediates of a periplasmic protein in which the protein and DsbA, a periplasmic disulfide bond-forming enzyme, are covalently linked by a disulfide bond. The cotranslational mixed-disulfide intermediate is, upon further chain elongation, resolved, releasing the oxidized polypeptide, thus allowing us to follow the folding process. This analysis reveals that two cysteines that are joined to form a structural disulfide can play different roles during the folding reaction and that the mode of translocation (cotranslational verse posttranslational) can affect the folding process of a protein in the periplasm. The latter finding leads us to propose that the activity of the ribosome (translation) can modulate protein folding even in an extracytosolic compartment.
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