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Pradhan S, Mirdha L, Sengupta T, Chakraborty H. Phosphatidylglycerol Acts as a Switch for Cholesterol-Dependent Membrane Binding of ApoE Signal Peptide. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:8126-8132. [PMID: 38568020 DOI: 10.1021/acs.langmuir.4c00178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
The apolipoprotein E (ApoE) signal peptide is a short stretch of N-terminal amino acids that direct the ApoE protein to the endoplasmic reticulum after synthesis. Previous studies have shown that this peptide can bind to lipid membranes in a cholesterol-dependent manner; however, the mechanism of this interaction is yet to be clarified. In this study, we aimed to investigate how the composition of neighboring lipids affects the membrane-binding of the ApoE signal peptide. We found that a negatively charged lipid, such as phosphatidylglycerol, can act as a switch that reduces the binding efficiency of the peptide to cholesterol-rich membranes. Interestingly, phosphatidylethanolamine does not activate the cholesterol-dependent binding of the ApoE signal peptide yet acts synergistically to enhance the cholesterol sensitivity in phosphatidylglycerol-containing membranes. To the best of our knowledge, this is the first report of modulation of the affinity of a peptide for a membrane by a neighboring lipid rather than by the lipid-binding domain of the peptide. Our findings revealed a novel role of lipid diversity in modulating the membrane binding of the ApoE signal peptide and its potential implications in the unidirectional trafficking of a newly synthesized protein from the ribosomes to the endoplasmic reticulum.
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Affiliation(s)
- Sasmita Pradhan
- School of Chemistry, Sambalpur University, Jyoti Vihar, Burla, Odisha 768 019, India
| | - Lipika Mirdha
- School of Chemistry, Sambalpur University, Jyoti Vihar, Burla, Odisha 768 019, India
| | - Tanusree Sengupta
- Department of Chemistry, Sri Sivasubramaniya Nadar College of Engineering, Chennai 603110, India
| | - Hirak Chakraborty
- School of Chemistry, Sambalpur University, Jyoti Vihar, Burla, Odisha 768 019, India
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2
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Madsen JJ, Yu W. Dynamic Nature of Staphylococcus aureus Type I Signal Peptidases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.23.576923. [PMID: 38328037 PMCID: PMC10849702 DOI: 10.1101/2024.01.23.576923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Molecular dynamics simulations are used to interrogate the dynamic nature of Staphylococcus aureus Type I signal peptidases, SpsA and SpsB, including the impact of the P29S mutation of SpsB. Fluctuations and plasticity- rigidity characteristics vary among the proteins, particularly in the extracellular domain. Intriguingly, the P29S mutation, which influences susceptibility to arylomycin antibiotics, affect the mechanically coupled motions in SpsB. The integrity of the active site is crucial for catalytic competency, and variations in sampled structural conformations among the proteins are consistent with diverse peptidase capabilities. We also explored the intricate interactions between the proteins and the model S. aureus membrane. It was observed that certain membrane-inserted residues in the loop around residue 50 (50s) and C-terminal loops, beyond the transmembrane domain, give rise to direct interactions with lipids in the bilayer membrane. Our findings are discussed in the context of functional knowledge about these signal peptidases, offering additional understanding of dynamic aspects relevant to some cellular processes with potential implications for drug targeting strategies.
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Affiliation(s)
- Jesper J. Madsen
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States of America
- Center for Global Health and Infectious Diseases Research, Global and Planetary Health, College of Public Health, University of South Florida, Tampa, Florida 33612, United States of America
| | - Wenqi Yu
- Department of Molecular Biosciences, College of Arts and Sciences, University of South Florida, Tampa, Florida 33612, United States of America
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3
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O’Neill P, Mistry RK, Brown AJ, James DC. Protein-Specific Signal Peptides for Mammalian Vector Engineering. ACS Synth Biol 2023; 12:2339-2352. [PMID: 37487508 PMCID: PMC10443038 DOI: 10.1021/acssynbio.3c00157] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Indexed: 07/26/2023]
Abstract
Expression of recombinant proteins in mammalian cell factories relies on synthetic assemblies of genetic parts to optimally control flux through the product biosynthetic pathway. In comparison to other genetic part-types, there is a relative paucity of characterized signal peptide components, particularly for mammalian cell contexts. In this study, we describe a toolkit of signal peptide elements, created using bioinformatics-led and synthetic design approaches, that can be utilized to enhance production of biopharmaceutical proteins in Chinese hamster ovary cell factories. We demonstrate, for the first time in a mammalian cell context, that machine learning can be used to predict how discrete signal peptide elements will perform when utilized to drive endoplasmic reticulum (ER) translocation of specific single chain protein products. For more complex molecular formats, such as multichain monoclonal antibodies, we describe how a combination of in silico and targeted design rule-based in vitro testing can be employed to rapidly identify product-specific signal peptide solutions from minimal screening spaces. The utility of this technology is validated by deriving vector designs that increase product titers ≥1.8×, compared to standard industry systems, for a range of products, including a difficult-to-express monoclonal antibody. The availability of a vastly expanded toolbox of characterized signal peptide parts, combined with streamlined in silico/in vitro testing processes, will permit efficient expression vector re-design to maximize titers of both simple and complex protein products.
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Affiliation(s)
- Pamela O’Neill
- Department
of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield S1 3JD, U.K.
| | - Rajesh K. Mistry
- AstraZeneca, BioPharmaceutical Development, Cell Culture and Fermentation
Sciences, Aaron Klugg Building, Granta
Park, Cambridge CB21 6GH, U.K.
| | - Adam J. Brown
- Department
of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield S1 3JD, U.K.
- SynGenSys
Limited, Freeths LLP, Norfolk Street, Sheffield S1 2JE, U.K.
| | - David C. James
- Department
of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield S1 3JD, U.K.
- SynGenSys
Limited, Freeths LLP, Norfolk Street, Sheffield S1 2JE, U.K.
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4
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Musik JE, Poole J, Day CJ, Haselhorst T, Jen FEC, Ve T, Masic V, Jennings MP, Zalucki YM. New Perspectives on Escherichia coli Signal Peptidase I Substrate Specificity: Investigating Why the TasA Cleavage Site Is Incompatible with LepB Cleavage. Microbiol Spectr 2023; 11:e0500522. [PMID: 37098897 PMCID: PMC10269814 DOI: 10.1128/spectrum.05005-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 04/10/2023] [Indexed: 04/27/2023] Open
Abstract
Escherichia coli signal peptidase I (LepB) has been shown to inefficiently cleave secreted proteins with aromatic amino acids at the second position after the signal peptidase cleavage site (P2'). The Bacillus subtilis exported protein TasA contains a phenylalanine at P2', which in B. subtilis is cleaved by a dedicated archaeal-organism-like signal peptidase, SipW. We have previously shown that when the TasA signal peptide is fused to maltose binding protein (MBP) up to the P2' position, the TasA-MBP fusion protein is cleaved very inefficiently by LepB. However, the precise reason why the TasA signal peptide hinders cleavage by LepB is not known. In this study, a set of 11 peptides were designed to mimic the inefficiently cleaved secreted proteins, wild-type TasA and TasA-MBP fusions, to determine whether the peptides interact with and inhibit the function of LepB. The binding affinity and inhibitory potential of the peptides against LepB were assessed by surface plasmon resonance (SPR) and a LepB enzyme activity assay. Molecular modeling of the interaction between TasA signal peptide and LepB indicated that the tryptophan residue at P2 (two amino acids before the cleavage site) inhibited the active site serine-90 residue on LepB from accessing the cleavage site. Replacing the P2 tryptophan with alanine (W26A) allowed for more efficient processing of the signal peptide when the TasA-MBP fusion was expressed in E. coli. The importance of this residue to inhibit signal peptide cleavage and the potential to design LepB inhibitors based on the TasA signal peptide are discussed. IMPORTANCE Signal peptidase I is an important drug target, and understanding its substrate is critically important to develop new bacterium-specific drugs. To that end, we have a unique signal peptide that we have shown is refractory to processing by LepB, the essential signal peptidase I in E. coli, but previously has been shown to be processed by a more human-like signal peptidase found in some bacteria. In this study, we demonstrate how the signal peptide can bind but is unable to be processed by LepB, using a variety of methods. This can inform the field on how to better design drugs that can target LepB and understand the differences between bacterial and human-like signal peptidases.
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Affiliation(s)
- Joanna E. Musik
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia
| | - Jessica Poole
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia
| | - Christopher J. Day
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia
| | - Thomas Haselhorst
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia
| | - Freda E.-C. Jen
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia
| | - Thomas Ve
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia
| | - Veronika Masic
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia
| | - Michael P. Jennings
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia
| | - Yaramah M. Zalucki
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia
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5
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Alias NAR, Hoo WPY, Siak PY, Othman SS, Mohammed Alitheen NB, In LLA, Abdul Rahim R, Song AAL. Effect of Secretion Efficiency of Mutant KRAS Neoantigen by Lactococcus lactis on the Immune Response of a Mucosal Vaccine Delivery Vehicle Targeting Colorectal Cancer. Int J Mol Sci 2023; 24:ijms24108928. [PMID: 37240273 DOI: 10.3390/ijms24108928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/06/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
Colorectal cancer (CRC) is often caused by mutations in the KRAS oncogene, making KRAS neoantigens a promising vaccine candidate for immunotherapy. Secreting KRAS antigens using live Generally Recognized as Safe (GRAS) vaccine delivery hosts such as Lactococcus lactis is deemed to be an effective strategy in inducing specific desired responses. Recently, through the engineering of a novel signal peptide SPK1 from Pediococcus pentosaceus, an optimized secretion system was developed in the L. lactis NZ9000 host. In this study, the potential of the L. lactis NZ9000 as a vaccine delivery host for the production of two KRAS oncopeptides (mutant 68V-DT and wild-type KRAS) through the use of the signal peptide SPK1 and its mutated derivative (SPKM19) was investigated. The expression and secretion efficiency analyses of KRAS peptides from L. lactis were performed in vitro and in vivo in BALB/c mice. Contradictory to our previous study using the reporter staphylococcal nuclease (NUC), the yield of secreted KRAS antigens mediated by the target mutant signal peptide SPKM19 was significantly lower (by ~1.3-folds) compared to the wild-type SPK1. Consistently, a superior elevation of IgA response against KRAS aided by SPK1 rather than mutant SPKM19 was observed. Despite the lower specific IgA response for SPKM19, a positive IgA immune response from mice intestinal washes was successfully triggered following immunization. Size and secondary conformation of the mature proteins are suggested to be the contributing factors for these discrepancies. This study proves the potential of L. lactis NZ9000 as a host for oral vaccine delivery due to its ability to evoke the desired mucosal immune response in the gastrointestinal tract of mice.
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Affiliation(s)
- Nur Aqlili Riana Alias
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia
| | - Winfrey Pui Yee Hoo
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Pui Yan Siak
- Faculty of Medicine and Health Sciences, UCSI University, Bandar Springhill, Port Dickson 71010, Malaysia
| | - Siti Sarah Othman
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia
- UPM-MAKNA Cancer Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Malaysia
| | - Noorjahan Banu Mohammed Alitheen
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia
- UPM-MAKNA Cancer Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Malaysia
| | - Lionel Lian Aun In
- Department of Biotechnology, Faculty of Applied Sciences, UCSI University Kuala Lumpur, Cheras 56000, Malaysia
| | - Raha Abdul Rahim
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia
- National Institutes of Biotechnology Malaysia, Argo-Biotechnology Institute Malaysia Complex, Serdang 43400, Malaysia
| | - Adelene Ai-Lian Song
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia
- Laboratory of Vaccine and Biomolecules, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Malaysia
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6
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Rasband SA, Bolton PE, Fang Q, Johnson PLF, Braun MJ. Evolution of the Growth Hormone Gene Duplication in Passerine Birds. Genome Biol Evol 2023; 15:7059008. [PMID: 36848146 PMCID: PMC10016047 DOI: 10.1093/gbe/evad033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 12/11/2022] [Accepted: 01/09/2023] [Indexed: 03/01/2023] Open
Abstract
Birds of the order Passeriformes represent the most speciose order of land vertebrates. Despite strong scientific interest in this super-radiation, genetic traits unique to passerines are not well characterized. A duplicate copy of growth hormone (GH) is the only gene known to be present in all major lineages of passerines, but not in other birds. GH genes plausibly influence extreme life history traits that passerines exhibit, including the shortest embryo-to-fledging developmental period of any avian order. To unravel the implications of this GH duplication, we investigated the molecular evolution of the ancestral avian GH gene (GH or GH1) and the novel passerine GH paralog (GH2), using 497 gene sequences extracted from 342 genomes. Passerine GH1 and GH2 are reciprocally monophyletic, consistent with a single duplication event from a microchromosome onto a macrochromosome in a common ancestor of extant passerines. Additional chromosomal rearrangements have changed the syntenic and potential regulatory context of these genes. Both passerine GH1 and GH2 display substantially higher rates of nonsynonymous codon change than non-passerine avian GH, suggesting positive selection following duplication. A site involved in signal peptide cleavage is under selection in both paralogs. Other sites under positive selection differ between the two paralogs, but many are clustered in one region of a 3D model of the protein. Both paralogs retain key functional features and are actively but differentially expressed in two major passerine suborders. These phenomena suggest that GH genes may be evolving novel adaptive roles in passerine birds.
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Affiliation(s)
- Shauna A Rasband
- Behavior, Ecology, Evolution and Systematics Graduate Program, University of Maryland, College Park, Maryland.,Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC
| | - Peri E Bolton
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC.,Department of Biology, East Carolina University, Greenville, North Carolina
| | - Qi Fang
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
| | | | - Michael J Braun
- Behavior, Ecology, Evolution and Systematics Graduate Program, University of Maryland, College Park, Maryland.,Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC
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7
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Grasso S, Dabene V, Hendriks MMW, Zwartjens P, Pellaux R, Held M, Panke S, van Dijl JM, Meyer A, van Rij T. Signal Peptide Efficiency: From High-Throughput Data to Prediction and Explanation. ACS Synth Biol 2023; 12:390-404. [PMID: 36649479 PMCID: PMC9942255 DOI: 10.1021/acssynbio.2c00328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The passage of proteins across biological membranes via the general secretory (Sec) pathway is a universally conserved process with critical functions in cell physiology and important industrial applications. Proteins are directed into the Sec pathway by a signal peptide at their N-terminus. Estimating the impact of physicochemical signal peptide features on protein secretion levels has not been achieved so far, partially due to the extreme sequence variability of signal peptides. To elucidate relevant features of the signal peptide sequence that influence secretion efficiency, an evaluation of ∼12,000 different designed signal peptides was performed using a novel miniaturized high-throughput assay. The results were used to train a machine learning model, and a post-hoc explanation of the model is provided. By describing each signal peptide with a selection of 156 physicochemical features, it is now possible to both quantify feature importance and predict the protein secretion levels directed by each signal peptide. Our analyses allow the detection and explanation of the relevant signal peptide features influencing the efficiency of protein secretion, generating a versatile tool for the de novo design and in silico evaluation of signal peptides.
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Affiliation(s)
- Stefano Grasso
- Department
of Medical Microbiology, University of Groningen,
University Medical Center Groningen, Hanzeplein 1, Groningen 9700 RB, The Netherlands,DSM
Biotechnology Center, Alexander Fleminglaan 1, Delft 2613 AX, Netherlands
| | - Valentina Dabene
- Department
of Biosystems Science and Engineering, ETH
Zurich, Mattenstrasse
26, Basel 4058, Switzerland,FGen
AG, Hochbergerstrasse
60C, Basel 4057, Switzerland
| | | | - Priscilla Zwartjens
- DSM
Biotechnology Center, Alexander Fleminglaan 1, Delft 2613 AX, Netherlands
| | - René Pellaux
- FGen
AG, Hochbergerstrasse
60C, Basel 4057, Switzerland
| | - Martin Held
- Department
of Biosystems Science and Engineering, ETH
Zurich, Mattenstrasse
26, Basel 4058, Switzerland
| | - Sven Panke
- Department
of Biosystems Science and Engineering, ETH
Zurich, Mattenstrasse
26, Basel 4058, Switzerland
| | - Jan Maarten van Dijl
- Department
of Medical Microbiology, University of Groningen,
University Medical Center Groningen, Hanzeplein 1, Groningen 9700 RB, The Netherlands,. Phone: +31503615187
| | - Andreas Meyer
- FGen
AG, Hochbergerstrasse
60C, Basel 4057, Switzerland
| | - Tjeerd van Rij
- DSM
Biotechnology Center, Alexander Fleminglaan 1, Delft 2613 AX, Netherlands,. Phone: +31628441843
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8
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Minagawa J, Dann M. Extracellular CahB1 from Sodalinema gerasimenkoae IPPAS B-353 Acts as a Functional Carboxysomal β-Carbonic Anhydrase in Synechocystis sp. PCC6803. PLANTS (BASEL, SWITZERLAND) 2023; 12:265. [PMID: 36678979 PMCID: PMC9865033 DOI: 10.3390/plants12020265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 12/27/2022] [Accepted: 01/03/2023] [Indexed: 06/17/2023]
Abstract
Cyanobacteria mostly rely on the active uptake of hydrated CO2 (i.e., bicarbonate ions) from the surrounding media to fuel their inorganic carbon assimilation. The dehydration of bicarbonate in close vicinity of RuBisCO is achieved through the activity of carboxysomal carbonic anhydrase (CA) enzymes. Simultaneously, many cyanobacterial genomes encode extracellular α- and β-class CAs (EcaA, EcaB) whose exact physiological role remains largely unknown. To date, the CahB1 enzyme of Sodalinema gerasimenkoae (formerly Microcoleus/Coleofasciculus chthonoplastes) remains the sole described active extracellular β-CA in cyanobacteria, but its molecular features strongly suggest it to be a carboxysomal rather than a secreted protein. Upon expression of CahB1 in Synechocystis sp. PCC6803, we found that its expression complemented the loss of endogenous CcaA. Moreover, CahB1 was found to localize to a carboxysome-harboring and CA-active cell fraction. Our data suggest that CahB1 retains all crucial properties of a cellular carboxysomal CA and that the secretion mechanism and/or the machinations of the Sodalinema gerasimenkoae carboxysome are different from those of Synechocystis.
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Affiliation(s)
- Jun Minagawa
- Division of Environmental Photobiology, National Institute for Basic Biology (NIBB), Aichi, Okazaki 444-8585, Japan
| | - Marcel Dann
- Division of Environmental Photobiology, National Institute for Basic Biology (NIBB), Aichi, Okazaki 444-8585, Japan
- Plant Molecular Biology, Ludwig-Maximilian University (LMU) Munich, 82152 Planegg, Germany
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9
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Xue S, Liu X, Pan Y, Xiao C, Feng Y, Zheng L, Zhao M, Huang M. Comprehensive Analysis of Signal Peptides in Saccharomyces cerevisiae Reveals Features for Efficient Secretion. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2203433. [PMID: 36478443 PMCID: PMC9839866 DOI: 10.1002/advs.202203433] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 11/10/2022] [Indexed: 05/30/2023]
Abstract
Signal peptides (SPs) are N-terminus sequences on the nascent polypeptide for protein export or localization delivery, which are essential for maintaining cell function. SPs are also employed as a key element for industrial production of secreted recombinant proteins. Yet, detailed information and rules about SPs and their cellular interactions are still not well understood. Here, systematic bioinformatics analysis and secretion capacity measurement of genome-wide SPs from the model organism Saccharomyces cerevisiae is performed. Several key features of SPs, including region properties, consensus motifs, evolutionary relationships, codon bias, e.g., are successfully revealed. Diverse cell metabolism can be trigged by using different SPs for heterologous protein secretion. Influences on SPs with different properties by chaperones can cause different secretory efficiencies. Protein secretion by the SP NCW2 in SEC72 deletion strain is 10 times than the control. These findings provide insights into the properties and functions of SPs and contribute to both fundamental research and industrial application.
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Affiliation(s)
- Songlyu Xue
- School of Food Science and EngineeringSouth China University of TechnologyGuangzhou510641China
- Guangdong Food Green Processing and Nutrition Regulation Technologies Research CenterGuangzhou510650China
| | - Xiufang Liu
- School of Food Science and EngineeringSouth China University of TechnologyGuangzhou510641China
- Guangdong Food Green Processing and Nutrition Regulation Technologies Research CenterGuangzhou510650China
| | - Yuyang Pan
- School of Food Science and EngineeringSouth China University of TechnologyGuangzhou510641China
- Guangdong Food Green Processing and Nutrition Regulation Technologies Research CenterGuangzhou510650China
| | - Chufan Xiao
- School of Food Science and EngineeringSouth China University of TechnologyGuangzhou510641China
- Guangdong Food Green Processing and Nutrition Regulation Technologies Research CenterGuangzhou510650China
| | - Yunzi Feng
- School of Food Science and EngineeringSouth China University of TechnologyGuangzhou510641China
- Guangdong Food Green Processing and Nutrition Regulation Technologies Research CenterGuangzhou510650China
| | - Lin Zheng
- School of Food Science and EngineeringSouth China University of TechnologyGuangzhou510641China
- Guangdong Food Green Processing and Nutrition Regulation Technologies Research CenterGuangzhou510650China
| | - Mouming Zhao
- School of Food Science and EngineeringSouth China University of TechnologyGuangzhou510641China
- Guangdong Food Green Processing and Nutrition Regulation Technologies Research CenterGuangzhou510650China
| | - Mingtao Huang
- School of Food Science and EngineeringSouth China University of TechnologyGuangzhou510641China
- Guangdong Food Green Processing and Nutrition Regulation Technologies Research CenterGuangzhou510650China
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10
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Zheng Y, Rajcsanyi LS, Kowalczyk M, Giuranna J, Herpertz-Dahlmann B, Seitz J, de Zwaan M, Herzog W, Ehrlich S, Zipfel S, Giel K, Egberts K, Burghardt R, Föcker M, Al-Lahham S, Hebebrand J, Fuhrer D, Tan S, Zwanziger D, Peters T, Hinney A. Lipocalin 2 - mutation screen and serum levels in patients with anorexia nervosa or obesity and in lean individuals. Front Endocrinol (Lausanne) 2023; 14:1137308. [PMID: 37025415 PMCID: PMC10071025 DOI: 10.3389/fendo.2023.1137308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 03/09/2023] [Indexed: 04/08/2023] Open
Abstract
CONTEXT The bone-derived adipokine lipocalin-2 is relevant for body weight regulation by stimulating the leptin-melanocortin pathway. OBJECTIVE We aimed to (i) detect variants in the lipocalin-2 gene (LCN2) which are relevant for body weight regulation and/or anorexia nervosa (AN); (ii) describe and characterize the impact of LCN2 and MC4R variants on circulating lipocalin-2 level. METHODS Sanger sequencing of the coding region of LCN2 in 284 children and adolescents with severe obesity or 287 patients with anorexia nervosa. In-silico analyses to evaluate functional implications of detected LCN2 variants. TaqMan assays for rare non-synonymous variants (NSVs) in additional independent study groups. Serum levels of lipocalin-2 were measured by ELISA in 35 females with NSVs in either LCN2 or MC4R, and 33 matched controls without NSVs in the two genes. RESULTS Fourteen LCN2-variants (five NSVs) were detected. LCN2-p.Leu6Pro and p.Gly9Val located in the highly conserved signal peptide region may induce functional consequences. The secondary structure change of lipocalin-2 due to LCN2-p.Val89Ile may decrease solubility and results in a low lipocalin-2 level in a heterozygotes carrier (female recovered from AN). Lean individuals had lower lipocalin-2 levels compared to patients with obesity (p = 0.033). CONCLUSION Lipocalin-2 levels are positively associated with body mass index (BMI). Single LCN2-variants might have a profound effect on lipocalin-2 levels.
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Affiliation(s)
- Yiran Zheng
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- Center for Translational Neuro- and Behavioral Sciences, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- *Correspondence: Yiran Zheng,
| | - Luisa Sophie Rajcsanyi
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- Center for Translational Neuro- and Behavioral Sciences, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Manuela Kowalczyk
- Department of Endocrinology, Diabetes and Metabolism and Clinical Chemistry – Division of Laboratory Research, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Johanna Giuranna
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Beate Herpertz-Dahlmann
- Department of Child and Adolescent Psychiatry and Psychotherapy, University Hospital of the RWTH Aachen, Aachen, Germany
| | - Jochen Seitz
- Department of Child and Adolescent Psychiatry and Psychotherapy, University Hospital of the RWTH Aachen, Aachen, Germany
| | - Martina de Zwaan
- Department of Psychosomatic Medicine and Psychotherapy, Hannover Medical School, Hannover, Germany
| | - Wolfgang Herzog
- Department of Internal Medicine II, General Internal and Psychosomatic Medicine, University of Heidelberg, Heidelberg, Germany
| | - Stefan Ehrlich
- Translational Developmental Neuroscience Section, Department of Child and Adolescent Psychiatry, TU-Dresden, University Hospital Carl Gustav Carus, Dresden University of Technology, Dresden, Germany
- Eating Disorders Research and Treatment Center, Department of Child and Adolescent Psychiatry, Faculty of Medicine, TU Dresden, Dresden, Germany
| | - Stephan Zipfel
- Department of Psychosomatic Medicine and Psychotherapy, Medical University Hospital, Tübingen, Germany
- Centre of Excellence for Eating Disorders, University of Tübingen, Tübingen, Germany
| | - Katrin Giel
- Department of Psychosomatic Medicine and Psychotherapy, Medical University Hospital, Tübingen, Germany
- Centre of Excellence for Eating Disorders, University of Tübingen, Tübingen, Germany
| | - Karin Egberts
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University of Würzburg, Würzburg, Germany
| | - Roland Burghardt
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, Oberberg Fachklinik Fasanenkiez, Berlin, Germany
| | - Manuel Föcker
- Department of Child and Adolescent Psychiatry, University of Münster, Münster, Germany
| | - Saad Al-Lahham
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, An-Najah National University, Nablus, Palestine
| | - Johannes Hebebrand
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- Center for Translational Neuro- and Behavioral Sciences, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Dagmar Fuhrer
- Department of Endocrinology, Diabetes and Metabolism and Clinical Chemistry – Division of Laboratory Research, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- Department of Endocrinology, Diabetes and Metabolism, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Susanne Tan
- Department of Endocrinology, Diabetes and Metabolism, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Denise Zwanziger
- Department of Endocrinology, Diabetes and Metabolism and Clinical Chemistry – Division of Laboratory Research, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Triinu Peters
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- Center for Translational Neuro- and Behavioral Sciences, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Anke Hinney
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- Center for Translational Neuro- and Behavioral Sciences, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
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11
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Optimization of Signal Peptide via Site-Directed Mutagenesis for Enhanced Secretion of Heterologous Proteins in Lactococcus lactis. Int J Mol Sci 2022; 23:ijms231710044. [PMID: 36077441 PMCID: PMC9456127 DOI: 10.3390/ijms231710044] [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] [Received: 08/01/2022] [Revised: 08/24/2022] [Accepted: 08/26/2022] [Indexed: 11/26/2022] Open
Abstract
Secretion efficiency of heterologous proteins in the Generally Regarded As Safe (GRAS) Lactococcus lactis is often reported to be insufficiently low due to limitations such as poor targeting and translocation by the signal peptide or degradation by the host proteases. In this study, the secretion efficiency in the host was enhanced through the utilization of a heterologous signal peptide (SP) SPK1 of Pediococcus pentosaceus. The SPK1 was subjected to site-directed mutations targeting its tripartite N-, H-, and C-domains, and the effect on secretion efficiency as compared to the wild-type SPK1 and native lactococcal USP45 was determined on a reporter nuclease (NUC) of Staphylococcus aureus. A Fluorescence Resonance Energy Transfer (FRET) analysis indicated that four out of eight SPK1 variants successfully enhanced the secretion of NUC, with the best mutant, SPKM19, showing elevated secretion efficiency up to 88% (or by 1.4-fold) and an improved secretion activity yield of 0.292 ± 0.122 U/mL (or by 1.7-fold) compared to the wild-type SPK1. Modifications of the SPK1 at the cleavage site C-domain region had successfully augmented the secretion efficiency. Meanwhile, mutations in the H-domain region had resulted in a detrimental effect on the NUC secretion. The development of heterologous SPs with better efficacy than the USP45 has been demonstrated in this study for enhanced secretion of heterologous production and mucosal delivery applications in the lactococcal host.
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12
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Holec PV, Camacho KV, Breuckman KC, Mou J, Birnbaum ME. Proteome-Scale Screening to Identify High-Expression Signal Peptides with Minimal N-Terminus Biases via Yeast Display. ACS Synth Biol 2022; 11:2405-2416. [PMID: 35687717 DOI: 10.1021/acssynbio.2c00101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Signal peptides are critical for the efficient expression and routing of extracellular and secreted proteins. Most protein production and screening technologies rely upon a relatively small set of signal peptides. Despite their central role in biotechnology, there are limited studies comprehensively examining the interplay between signal peptides and expressed protein sequences. Here, we describe a high-throughput method to screen novel signal peptides that maintain a high degree of surface expression across a range of protein scaffolds with highly variable N-termini. We find that the canonical signal peptide used in yeast surface display, derived from Aga2p, fails to achieve high surface expression for 42.5% of constructs containing diverse N-termini. To circumvent this, we have identified two novel signal peptides derived from endogenous yeast proteins, SRL1 and KISH, which are highly tolerant to diverse N-terminal sequences. This pipeline can be used to expand our understanding of signal peptide function, identify improved signal peptides for protein expression, and refine the computational tools used for signal peptide prediction.
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Affiliation(s)
- Patrick V Holec
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Karen V Camacho
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Kathryn C Breuckman
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Jody Mou
- Harvard-MIT Program in Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Michael E Birnbaum
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.,Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts 02139, United States
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13
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Qin X, Li S, Li X, Pei D, Liu Y, Ding Y, Liu L, Bi H, Shi X, Guo Y, Fang E, Huang F, Yu L, Zhu L, An Y, Valencia CA, Li Y, Dong B, Zhou Y. Development of an Adeno-Associated Virus-Vectored SARS-CoV-2 Vaccine and Its Immunogenicity in Mice. Front Cell Infect Microbiol 2022; 12:802147. [PMID: 35310850 PMCID: PMC8927296 DOI: 10.3389/fcimb.2022.802147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 02/08/2022] [Indexed: 12/12/2022] Open
Abstract
Owing to the outbreak of the novel coronavirus (SARS-CoV-2) worldwide at the end of 2019, the development of a SARS-CoV-2 vaccine became an urgent need. In this study, we developed a type 9 adeno-associated virus vectored vaccine candidate expressing a dimeric receptor binding domain (RBD) of the SARS-CoV-2 spike protein (S protein) and evaluated its immunogenicity in a murine model. The vaccine candidate, named AAV9-RBD virus, was constructed by inserting a signal peptide to the N-terminus of two copies of RBD, spaced by a linker, into the genome of a type 9 adeno-associated virus. In vitro assays showed that HeLa cells infected by the recombinant AAV virus expressed high levels of the recombinant RBD protein, mostly found in the cell culture supernatant. The recombinant AAV9-RBD virus was cultured and purified. The genome titer of the purified recombinant AAV9-RBD virus was determined to be 2.4 × 1013 genome copies/mL (GC/mL) by Q-PCR. Balb/c mice were immunized with the virus by intramuscular injection or nasal drip administration. Eight weeks after immunization, neutralizing antibodies against the new coronavirus pseudovirus were detected in the sera of all mice; the mean neutralizing antibody EC50 values were 517.7 ± 292.1 (n=10) and 682.8 ± 454.0 (n=10) in the intramuscular injection group and nasal drip group, respectively. The results of this study showed that the recombinant AAV9-RBD virus may be used for the development of a SARS-CoV-2 vaccine.
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Affiliation(s)
- Xi Qin
- Department of Recombinant Products, National Institutes for Food and Drug Control, Beijing, China
| | - Shanhu Li
- Department of Cell Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Xiang Li
- Department of Recombinant Products, National Institutes for Food and Drug Control, Beijing, China
| | - Dening Pei
- Department of Recombinant Products, National Institutes for Food and Drug Control, Beijing, China
| | - Yu Liu
- Department of Geriatrics and National Clinical Research Center for Geriatrics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Youxue Ding
- Department of Recombinant Products, National Institutes for Food and Drug Control, Beijing, China
| | - Lan Liu
- Department of Recombinant Products, National Institutes for Food and Drug Control, Beijing, China
| | - Hua Bi
- Department of Recombinant Products, National Institutes for Food and Drug Control, Beijing, China
| | - Xinchang Shi
- Department of Recombinant Products, National Institutes for Food and Drug Control, Beijing, China
| | - Ying Guo
- Department of Recombinant Products, National Institutes for Food and Drug Control, Beijing, China
| | - Enyue Fang
- Department of Arboviral Vaccine, National Institutes for Food and Drug Control, Beijing, China
| | - Fang Huang
- Department of Cell Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Lei Yu
- Department of Recombinant Products, National Institutes for Food and Drug Control, Beijing, China
| | - Liuqiang Zhu
- Department of Recombinant Products, National Institutes for Food and Drug Control, Beijing, China
| | - Yifang An
- Department of Recombinant Products, National Institutes for Food and Drug Control, Beijing, China
| | - C. Alexander Valencia
- Department of Geriatrics and National Clinical Research Center for Geriatrics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Yuhua Li
- Department of Arboviral Vaccine, National Institutes for Food and Drug Control, Beijing, China
- *Correspondence: Yuhua Li, ; Biao Dong, ; Yong Zhou,
| | - Biao Dong
- Department of Geriatrics and National Clinical Research Center for Geriatrics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
- *Correspondence: Yuhua Li, ; Biao Dong, ; Yong Zhou,
| | - Yong Zhou
- Department of Recombinant Products, National Institutes for Food and Drug Control, Beijing, China
- *Correspondence: Yuhua Li, ; Biao Dong, ; Yong Zhou,
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14
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D’Ippolito R, Drew MR, Mehalko J, Snead K, Wall V, Putman Z, Esposito D, DeHart CJ. Refining the N-Termini of the SARS-CoV-2 Spike Protein and Its Discrete Receptor-Binding Domain. J Proteome Res 2021; 20:4427-4434. [PMID: 34379411 PMCID: PMC8419861 DOI: 10.1021/acs.jproteome.1c00349] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Indexed: 01/07/2023]
Abstract
Previous work employing five SARS-CoV-2 spike protein receptor-binding domain (RBD) constructs, comprising versions originally developed by Mt. Sinai or the Ragon Institute and later optimized in-house, revealed potential heterogeneity which led to questions regarding variable seropositivity assay performance. Each construct was subjected to N-deglycosylation and subsequent intact mass analysis, revealing significant deviations from predicted theoretical mass for all five proteins. Complementary tandem MS/MS analysis revealed the presence of an additional pyroGlu residue on the N-termini of the two Mt. Sinai RBD constructs, as well as on the N-terminus of the full-length spike protein from which they were derived, thus explaining the observed mass shift and definitively establishing the spike protein N-terminal sequence. Moreover, the observed mass additions for the three Ragon Institute RBD constructs were identified as variable N-terminal cleavage points within the signal peptide sequence employed for recombinant expression. To resolve this issue and minimize heterogeneity for further seropositivity assay development, the best-performing RBD construct was further optimized to exhibit complete homogeneity, as determined by both intact mass and tandem MS/MS analysis. This new RBD construct has been validated for seropositivity assay performance, is available to the greater scientific community, and is recommended for use in future assay development.
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Affiliation(s)
- Robert
A. D’Ippolito
- NCI RAS Initiative, Cancer
Research Technology Program, Frederick National
Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Matthew R. Drew
- NCI RAS Initiative, Cancer
Research Technology Program, Frederick National
Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Jennifer Mehalko
- NCI RAS Initiative, Cancer
Research Technology Program, Frederick National
Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Kelly Snead
- NCI RAS Initiative, Cancer
Research Technology Program, Frederick National
Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Vanessa Wall
- NCI RAS Initiative, Cancer
Research Technology Program, Frederick National
Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Zoe Putman
- NCI RAS Initiative, Cancer
Research Technology Program, Frederick National
Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Dominic Esposito
- NCI RAS Initiative, Cancer
Research Technology Program, Frederick National
Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Caroline J. DeHart
- NCI RAS Initiative, Cancer
Research Technology Program, Frederick National
Laboratory for Cancer Research, Frederick, Maryland 21702, United States
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15
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Yim C, Chung Y, Kim J, Nilsson I, Kim JS, Kim H. Spc1 regulates the signal peptidase-mediated processing of membrane proteins. J Cell Sci 2021; 134:269144. [PMID: 34125229 PMCID: PMC8277137 DOI: 10.1242/jcs.258936] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 06/01/2021] [Indexed: 11/20/2022] Open
Abstract
Signal peptidase (SPase) cleaves the signal sequences (SSs) of secretory precursors. It contains an evolutionarily conserved membrane protein subunit, Spc1, that is dispensable for the catalytic activity of SPase and whose role remains unknown. In this study, we investigated the function of yeast Spc1. First, we set up an in vivo SPase cleavage assay using variants of the secretory protein carboxypeptidase Y (CPY) with SSs modified in the N-terminal and hydrophobic core regions. When comparing the SS cleavage efficiencies of these variants in cells with or without Spc1, we found that signal-anchored sequences became more susceptible to cleavage by SPase without Spc1. Furthermore, SPase-mediated processing of model membrane proteins was enhanced in the absence of Spc1 and was reduced upon overexpression of Spc1. Spc1 co-immunoprecipitated with proteins carrying uncleaved signal-anchored or transmembrane (TM) segments. Taken together, these results suggest that Spc1 protects TM segments from SPase action, thereby sharpening SPase substrate selection and acting as a negative regulator of the SPase-mediated processing of membrane proteins.
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Affiliation(s)
- Chewon Yim
- School of Biological Sciences and Institute of Microbiology , Seoul National University, Seoul 08826, South Korea
| | - Yeonji Chung
- School of Biological Sciences and Institute of Microbiology , Seoul National University, Seoul 08826, South Korea
| | - Jeesoo Kim
- School of Biological Sciences and Institute of Microbiology , Seoul National University, Seoul 08826, South Korea.,Center for RNA Research , Institute for Basic Science, Seoul 08826, South Korea
| | - IngMarie Nilsson
- Department of Biochemistry and Biophysics, Stockholm University, SE-10691 Stockholm, Sweden
| | - Jong-Seo Kim
- School of Biological Sciences and Institute of Microbiology , Seoul National University, Seoul 08826, South Korea.,Center for RNA Research , Institute for Basic Science, Seoul 08826, South Korea
| | - Hyun Kim
- School of Biological Sciences and Institute of Microbiology , Seoul National University, Seoul 08826, South Korea
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16
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Mullin MJ, Wilkinson C, Hiles I, Smith KJ. Improved secretion of recombinant human IL-25 in HEK293 cells using a signal peptide-pro-peptide domain derived from Trypsin-1. Biotechnol Lett 2021; 43:757-765. [PMID: 33415569 DOI: 10.1007/s10529-020-03072-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 12/14/2020] [Indexed: 11/28/2022]
Abstract
OBJECTIVE To compare the effects of human Trypsin-1 signal peptide and pro-peptide on the expression and secretion efficiency of human Interleukin-25 from mammalian cells. RESULTS The signal peptide and combined signal peptide-pro-peptide sequence of human Trypsin-1 improved the secretion of human IL-25 from 1.7 to 3.2 µg/ml and 1.7 to 8.2 µg/ml, respectively. Deletion analysis identified the minimal Trypsin-1 derived secretion domain that maintains improved human Interleukin-25 production and secretion. The presence of Trypsin-1 pro-peptide sequence does not affect the function of secreted human Interleukin-25. CONCLUSION The Trypsin-1 signal peptide-pro-peptide sequence increased human IL-25 expression and secretion in mammalian cells by fivefold.
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Affiliation(s)
- Michael J Mullin
- Protein Technologies Group, GlaxoSmithKline Research & Development, Gunnels Wood Road, Stevenage, SG1 2NY, Hertfordshire, UK. .,Department of Protein & Cellular Sciences, GlaxoSmithKline Research & Development, Gunnels Wood Road, Stevenage, SG1 2NY, Hertfordshire, UK.
| | - Claire Wilkinson
- Protein Technologies Group, GlaxoSmithKline Research & Development, Gunnels Wood Road, Stevenage, SG1 2NY, Hertfordshire, UK.,Department of Protein & Cellular Sciences, GlaxoSmithKline Research & Development, Gunnels Wood Road, Stevenage, SG1 2NY, Hertfordshire, UK
| | - Ian Hiles
- Reagent Design Group, GlaxoSmithKline Research & Development, Gunnels Wood Road, Stevenage, SG1 2NY, Hertfordshire, UK.,Department of Protein & Cellular Sciences, GlaxoSmithKline Research & Development, Gunnels Wood Road, Stevenage, SG1 2NY, Hertfordshire, UK
| | - Kathrine J Smith
- Department of Protein & Cellular Sciences, GlaxoSmithKline Research & Development, Gunnels Wood Road, Stevenage, SG1 2NY, Hertfordshire, UK
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17
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Braun R, Schönberger N, Vinke S, Lederer F, Kalinowski J, Pollmann K. Application of Next Generation Sequencing (NGS) in Phage Displayed Peptide Selection to Support the Identification of Arsenic-Binding Motifs. Viruses 2020; 12:E1360. [PMID: 33261041 PMCID: PMC7759992 DOI: 10.3390/v12121360] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/16/2020] [Accepted: 11/24/2020] [Indexed: 11/21/2022] Open
Abstract
Next generation sequencing (NGS) in combination with phage surface display (PSD) are powerful tools in the newly equipped molecular biology toolbox for the identification of specific target binding biomolecules. Application of PSD led to the discovery of manifold ligands in clinical and material research. However, limitations of traditional phage display hinder the identification process. Growth-based library biases and target-unrelated peptides often result in the dominance of parasitic sequences and the collapse of library diversity. This study describes the effective enrichment of specific peptide motifs potentially binding to arsenic as proof-of-concept using the combination of PSD and NGS. Arsenic is an environmental toxin, which is applied in various semiconductors as gallium arsenide and selective recovery of this element is crucial for recycling and remediation. The development of biomolecules as specific arsenic-binding sorbents is a new approach for its recovery. Usage of NGS for all biopanning fractions allowed for evaluation of motif enrichment, in-depth insight into the selection process and the discrimination of biopanning artefacts, e.g., the amplification-induced library-wide reduction in hydrophobic amino acid proportion. Application of bioinformatics tools led to the identification of an SxHS and a carboxy-terminal QxQ motif, which are potentially involved in the binding of arsenic. To the best of our knowledge, this is the first report of PSD combined with NGS of all relevant biopanning fractions.
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Affiliation(s)
- Robert Braun
- Department of Biotechnology, Helmholtz Institute Freiberg for Resource Technology, Helmholtz Center Dresden-Rossendorf, 01328 Dresden, Germany; (N.S.); (F.L.); (K.P.)
| | - Nora Schönberger
- Department of Biotechnology, Helmholtz Institute Freiberg for Resource Technology, Helmholtz Center Dresden-Rossendorf, 01328 Dresden, Germany; (N.S.); (F.L.); (K.P.)
| | - Svenja Vinke
- Microbial Genomics and Biotechnology, CeBiTec–Center for Biotechnology, Bielefeld University, 33594 Bielefeld, Germany; (S.V.); (J.K.)
| | - Franziska Lederer
- Department of Biotechnology, Helmholtz Institute Freiberg for Resource Technology, Helmholtz Center Dresden-Rossendorf, 01328 Dresden, Germany; (N.S.); (F.L.); (K.P.)
| | - Jörn Kalinowski
- Microbial Genomics and Biotechnology, CeBiTec–Center for Biotechnology, Bielefeld University, 33594 Bielefeld, Germany; (S.V.); (J.K.)
| | - Katrin Pollmann
- Department of Biotechnology, Helmholtz Institute Freiberg for Resource Technology, Helmholtz Center Dresden-Rossendorf, 01328 Dresden, Germany; (N.S.); (F.L.); (K.P.)
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18
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Li R, Zeng W, Ma M, Wei Z, Liu H, Liu X, Wang M, Shi X, Zeng J, Yang L, Mo D, Liu X, Chen Y, He Z. Precise editing of myostatin signal peptide by CRISPR/Cas9 increases the muscle mass of Liang Guang Small Spotted pigs. Transgenic Res 2020; 29:149-163. [PMID: 31927726 DOI: 10.1007/s11248-020-00188-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 01/04/2020] [Indexed: 12/17/2022]
Abstract
Myostatin (MSTN), a member of the transforming growth factor-β superfamily, is a negative regulator of muscle growth and development. Disruption of the MSTN gene in various mammalian species markedly promotes muscle growth. Previous studies have mainly focused on the disruption of the MSTN peptide coding region in pigs but not on the modification of the signal peptide region. In this study, the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated protein 9 (Cas9) system was used to successfully introduce two mutations (PVD20H and GP19del) in the MSTN signal peptide region of the indigenous Chinese pig breed, Liang Guang Small Spotted pig. Both mutations in signal peptide increased the muscle mass without inhibiting the production of mature MSTN peptide in the cells. Histological analysis revealed that the enhanced muscle mass in MSTN+/PVD20H pig was mainly due to an increase in the number of muscle fibers. The expression of MSTN in the longissimus dorsi muscle of MSTN+/PVD20H and MSTNKO/PVD20H pigs was significantly downregulated, whereas that of myogenic regulatory factors, including MyoD, Myogenin, and Myf-5, was significantly upregulated when compared to those in the longissimus dorsi muscle of wild-type pigs. Meanwhile, the mutations also activated the PI3K/Akt pathway. The results of this study indicated that precise editing of the MSTN signal peptide can enhance porcine muscle development without markedly affecting the expression of mature MSTN peptide, which could exert other beneficial biological functions in the edited pigs.
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Affiliation(s)
- Ruiqiang Li
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, No. 3 Road of Higher Education Mega Centre North, Guangzhou, 510006, People's Republic of China
| | - Wu Zeng
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, No. 3 Road of Higher Education Mega Centre North, Guangzhou, 510006, People's Republic of China
| | - Miao Ma
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, No. 3 Road of Higher Education Mega Centre North, Guangzhou, 510006, People's Republic of China
| | - Zixuan Wei
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, No. 3 Road of Higher Education Mega Centre North, Guangzhou, 510006, People's Republic of China
| | - Hongbo Liu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, No. 3 Road of Higher Education Mega Centre North, Guangzhou, 510006, People's Republic of China
| | - Xiaofeng Liu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, No. 3 Road of Higher Education Mega Centre North, Guangzhou, 510006, People's Republic of China
| | - Min Wang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, No. 3 Road of Higher Education Mega Centre North, Guangzhou, 510006, People's Republic of China
| | - Xuan Shi
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, No. 3 Road of Higher Education Mega Centre North, Guangzhou, 510006, People's Republic of China
| | - Jianhua Zeng
- Guangdong YIHAO Food Co., Ltd., Guangzhou, 510620, People's Republic of China
| | - Linfang Yang
- Guangdong YIHAO Food Co., Ltd., Guangzhou, 510620, People's Republic of China
| | - Delin Mo
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, No. 3 Road of Higher Education Mega Centre North, Guangzhou, 510006, People's Republic of China
| | - Xiaohong Liu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, No. 3 Road of Higher Education Mega Centre North, Guangzhou, 510006, People's Republic of China
| | - Yaosheng Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, No. 3 Road of Higher Education Mega Centre North, Guangzhou, 510006, People's Republic of China
| | - Zuyong He
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, No. 3 Road of Higher Education Mega Centre North, Guangzhou, 510006, People's Republic of China.
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19
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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 2018; 8:488. [PMID: 30498661 DOI: 10.1007/s13205-018-1517-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Accepted: 11/13/2018] [Indexed: 12/30/2022] Open
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.
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Affiliation(s)
- Hajar Owji
- 1Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
- 2Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Shiva Hemmati
- 1Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
- 2Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
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20
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Liu M, Weiss MA, Arunagiri A, Yong J, Rege N, Sun J, Haataja L, Kaufman RJ, Arvan P. Biosynthesis, structure, and folding of the insulin precursor protein. Diabetes Obes Metab 2018; 20 Suppl 2:28-50. [PMID: 30230185 PMCID: PMC6463291 DOI: 10.1111/dom.13378] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 05/04/2018] [Accepted: 05/23/2018] [Indexed: 02/06/2023]
Abstract
Insulin synthesis in pancreatic β-cells is initiated as preproinsulin. Prevailing glucose concentrations, which oscillate pre- and postprandially, exert major dynamic variation in preproinsulin biosynthesis. Accompanying upregulated translation of the insulin precursor includes elements of the endoplasmic reticulum (ER) translocation apparatus linked to successful orientation of the signal peptide, translocation and signal peptide cleavage of preproinsulin-all of which are necessary to initiate the pathway of proper proinsulin folding. Evolutionary pressures on the primary structure of proinsulin itself have preserved the efficiency of folding ("foldability"), and remarkably, these evolutionary pressures are distinct from those protecting the ultimate biological activity of insulin. Proinsulin foldability is manifest in the ER, in which the local environment is designed to assist in the overall load of proinsulin folding and to favour its disulphide bond formation (while limiting misfolding), all of which is closely tuned to ER stress response pathways that have complex (beneficial, as well as potentially damaging) effects on pancreatic β-cells. Proinsulin misfolding may occur as a consequence of exuberant proinsulin biosynthetic load in the ER, proinsulin coding sequence mutations, or genetic predispositions that lead to an altered ER folding environment. Proinsulin misfolding is a phenotype that is very much linked to deficient insulin production and diabetes, as is seen in a variety of contexts: rodent models bearing proinsulin-misfolding mutants, human patients with Mutant INS-gene-induced Diabetes of Youth (MIDY), animal models and human patients bearing mutations in critical ER resident proteins, and, quite possibly, in more common variety type 2 diabetes.
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Affiliation(s)
- Ming Liu
- Department of Endocrinology and Metabolism, Tianjin Medical University General Hospital, Tianjin, China 300052
- Division of Metabolism, Endocrinology & Diabetes, University of Michigan Medical School, Ann Arbor 48105 MI USA
| | - Michael A. Weiss
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis 46202 IN USA
- Department of Biochemistry, Case-Western Reserve University, Cleveland 44016 OH USA
| | - Anoop Arunagiri
- Division of Metabolism, Endocrinology & Diabetes, University of Michigan Medical School, Ann Arbor 48105 MI USA
| | - Jing Yong
- Degenerative Diseases Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92307 USA
| | - Nischay Rege
- Department of Biochemistry, Case-Western Reserve University, Cleveland 44016 OH USA
| | - Jinhong Sun
- Department of Endocrinology and Metabolism, Tianjin Medical University General Hospital, Tianjin, China 300052
- Division of Metabolism, Endocrinology & Diabetes, University of Michigan Medical School, Ann Arbor 48105 MI USA
| | - Leena Haataja
- Division of Metabolism, Endocrinology & Diabetes, University of Michigan Medical School, Ann Arbor 48105 MI USA
| | - Randal J. Kaufman
- Degenerative Diseases Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92307 USA
| | - Peter Arvan
- Division of Metabolism, Endocrinology & Diabetes, University of Michigan Medical School, Ann Arbor 48105 MI USA
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21
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Vahedi F, Nassiri M, Ghovvati S, Javadmanesh A. Evaluation of Different Signal Peptides Using Bioinformatics Tools to Express Recombinant Erythropoietin in Mammalian Cells. Int J Pept Res Ther 2018. [DOI: 10.1007/s10989-018-9746-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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22
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Lindert U, Gnoli M, Maioli M, Bedeschi MF, Sangiorgi L, Rohrbach M, Giunta C. Insight into the Pathology of a COL1A1 Signal Peptide Heterozygous Mutation Leading to Severe Osteogenesis Imperfecta. Calcif Tissue Int 2018; 102:373-379. [PMID: 29101475 PMCID: PMC5818590 DOI: 10.1007/s00223-017-0359-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 10/30/2017] [Indexed: 12/22/2022]
Abstract
Osteogenesis imperfecta or "brittle bone disease" is a congenital disorder of connective tissue causing the bone to break easily. Around 85-90% of cases are due to autosomal dominant mutations in the genes encoding type I collagen, the major organic component of bone. Genotype-phenotype correlations have shown that quantitative defects of collagen type I lead to mild OI, whereas structural defects show a wide clinical range from mild to perinatal lethal. This may partially be explained by the type of amino acid substitution and the relative location in the domain structure. To fully understand the variability of the clinical manifestation and the underlying pathomechanisms, further investigations are required. Here we provide the first biochemical characterization of a mutation at the signal peptide cleavage site of COL1A1, a domain not yet characterized. By steady-state analysis, we observed reduced production of collagen type I. Furthermore, by pulse-chase analysis we detected delayed secretion and partial intracellular retention of collagen I. In the cellular fraction, the electrophoretic migration was abnormal; however, secreted type I collagen showed a normal migration pattern. The intracellular retention of collagen I was confirmed by immunofluorescent staining. Moreover, transmission electron microscopy of cultured fibroblasts revealed enlargement of ER cisternae. These results further support the hypothesis that mechanisms interfering with ER integrity play an important role in the pathology of severe OI.
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Affiliation(s)
- U Lindert
- Connective Tissue Unit, Division of Metabolism and Children's Research Center, University Children's Hospital, Steinwiesstrasse 75, 8032, Zurich, Switzerland
| | - M Gnoli
- Department of Medical Genetics and Skeletal Rare Diseases, Rizzoli Orthopaedic Institute, Bologna, Italy
| | - M Maioli
- Department of Medical Genetics and Skeletal Rare Diseases, Rizzoli Orthopaedic Institute, Bologna, Italy
| | - M F Bedeschi
- Medical Genetics Unit, Fondazione IRCCS Ca'Granda Ospedale Maggiore Policlinico, Milano, Italy
| | - L Sangiorgi
- Department of Medical Genetics and Skeletal Rare Diseases, Rizzoli Orthopaedic Institute, Bologna, Italy
| | - M Rohrbach
- Connective Tissue Unit, Division of Metabolism and Children's Research Center, University Children's Hospital, Steinwiesstrasse 75, 8032, Zurich, Switzerland
| | - C Giunta
- Connective Tissue Unit, Division of Metabolism and Children's Research Center, University Children's Hospital, Steinwiesstrasse 75, 8032, Zurich, Switzerland.
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23
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Guo H, Sun J, Li X, Xiong Y, Wang H, Shu H, Zhu R, Liu Q, Huang Y, Madley R, Wang Y, Cui J, Arvan P, Liu M. Positive charge in the n-region of the signal peptide contributes to efficient post-translational translocation of small secretory preproteins. J Biol Chem 2017; 293:1899-1907. [PMID: 29229776 DOI: 10.1074/jbc.ra117.000922] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 11/30/2017] [Indexed: 12/17/2022] Open
Abstract
Increasing evidence indicates that many small secretory preproteins can undergo post-translational translocation across the membrane of the endoplasmic reticulum. Although the cellular machinery involved in post-translational translocation of small secretory preproteins has begun to be elucidated, the intrinsic signals contained within these small secretory preproteins that contribute to their efficient post-translational translocation remain unknown. Here, we analyzed the eukaryotic secretory proteome and discovered the small secretory preproteins tend to have a higher probability to harbor the positive charge in the n-region of the signal peptide (SP). Eliminating the positive charge of the n-region blocked post-translational translocation of newly synthesized preproteins and selectively impaired translocation efficiency of small secretory preproteins. The pathophysiological significance of the positive charge in the n-region of SP was underscored by recently identified preproinsulin SP mutations that impair translocation of preproinsulin and cause maturity onset diabetes of youth (MODY). Remarkably, we have found that slowing the polypeptide elongation rate of small secretory preproteins could alleviate the translocation defect caused by loss of the n-region positive charge of the signal peptide. Together, these data reveal not only a previously unrecognized role of the n-region's positive charge in ensuring efficient post-translational translocation of small secretory preproteins, but they also highlight the molecular contribution of defects in this process to the pathogenesis of genetic disorders such as MODY.
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Affiliation(s)
- Huan Guo
- From the Department of Endocrinology and Metabolism, Tianjin Medical University General Hospital, Tianjin 300052, China.,the Division of Metabolism, Endocrinology and Diabetes, University of Michigan Medical School, Ann Arbor, Michigan 48105, and
| | - Jinhong Sun
- From the Department of Endocrinology and Metabolism, Tianjin Medical University General Hospital, Tianjin 300052, China.,the Division of Metabolism, Endocrinology and Diabetes, University of Michigan Medical School, Ann Arbor, Michigan 48105, and
| | - Xin Li
- From the Department of Endocrinology and Metabolism, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Yi Xiong
- the Division of Metabolism, Endocrinology and Diabetes, University of Michigan Medical School, Ann Arbor, Michigan 48105, and
| | - Heting Wang
- From the Department of Endocrinology and Metabolism, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Hua Shu
- From the Department of Endocrinology and Metabolism, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Ruimin Zhu
- From the Department of Endocrinology and Metabolism, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Qi Liu
- From the Department of Endocrinology and Metabolism, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Yumeng Huang
- From the Department of Endocrinology and Metabolism, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Rachel Madley
- the Division of Metabolism, Endocrinology and Diabetes, University of Michigan Medical School, Ann Arbor, Michigan 48105, and
| | - Yulun Wang
- the Division of Endocrinology, Tianjin People's Hospital, Tianjin 300120, China
| | - Jingqiu Cui
- From the Department of Endocrinology and Metabolism, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Peter Arvan
- the Division of Metabolism, Endocrinology and Diabetes, University of Michigan Medical School, Ann Arbor, Michigan 48105, and
| | - Ming Liu
- From the Department of Endocrinology and Metabolism, Tianjin Medical University General Hospital, Tianjin 300052, China, .,the Division of Metabolism, Endocrinology and Diabetes, University of Michigan Medical School, Ann Arbor, Michigan 48105, and
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24
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Snapp EL, McCaul N, Quandte M, Cabartova Z, Bontjer I, Källgren C, Nilsson I, Land A, von Heijne G, Sanders RW, Braakman I. Structure and topology around the cleavage site regulate post-translational cleavage of the HIV-1 gp160 signal peptide. eLife 2017; 6:26067. [PMID: 28753126 PMCID: PMC5577925 DOI: 10.7554/elife.26067] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 07/26/2017] [Indexed: 12/29/2022] Open
Abstract
Like all other secretory proteins, the HIV-1 envelope glycoprotein gp160 is targeted to the endoplasmic reticulum (ER) by its signal peptide during synthesis. Proper gp160 folding in the ER requires core glycosylation, disulfide-bond formation and proline isomerization. Signal-peptide cleavage occurs only late after gp160 chain termination and is dependent on folding of the soluble subunit gp120 to a near-native conformation. We here detail the mechanism by which co-translational signal-peptide cleavage is prevented. Conserved residues from the signal peptide and residues downstream of the canonical cleavage site form an extended alpha-helix in the ER membrane, which covers the cleavage site, thus preventing cleavage. A point mutation in the signal peptide breaks the alpha helix allowing co-translational cleavage. We demonstrate that postponed cleavage of gp160 enhances functional folding of the molecule. The change to early cleavage results in decreased viral fitness compared to wild-type HIV.
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Affiliation(s)
- Erik Lee Snapp
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Nicholas McCaul
- Cellular Protein Chemistry, Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Matthias Quandte
- Cellular Protein Chemistry, Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Zuzana Cabartova
- National Institute of Public Health, National Reference Laboratory for Viral Hepatitis, Prague, Czech Republic
| | - Ilja Bontjer
- Department of Medical Microbiology, Laboratory of Experimental Virology, Center for Infection and Immunity Amsterdam, Academic Medical Center, Amsterdam, Netherlands
| | - Carolina Källgren
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.,Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - IngMarie Nilsson
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.,Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Aafke Land
- Cellular Protein Chemistry, Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Gunnar von Heijne
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.,Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Rogier W Sanders
- Department of Medical Microbiology, Laboratory of Experimental Virology, Center for Infection and Immunity Amsterdam, Academic Medical Center, Amsterdam, Netherlands
| | - Ineke Braakman
- Cellular Protein Chemistry, Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, Utrecht, Netherlands
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25
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Bland MJ, Ducos-Galand M, Val ME, Mazel D. An att site-based recombination reporter system for genome engineering and synthetic DNA assembly. BMC Biotechnol 2017; 17:62. [PMID: 28705159 PMCID: PMC5512741 DOI: 10.1186/s12896-017-0382-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 07/09/2017] [Indexed: 11/25/2022] Open
Abstract
Background Direct manipulation of the genome is a widespread technique for genetic studies and synthetic biology applications. The tyrosine and serine site-specific recombination systems of bacteriophages HK022 and ΦC31 are widely used for stable directional exchange and relocation of DNA sequences, making them valuable tools in these contexts. We have developed site-specific recombination tools that allow the direct selection of recombination events by embedding the attB site from each system within the β-lactamase resistance coding sequence (bla). Results The HK and ΦC31 tools were developed by placing the attB sites from each system into the signal peptide cleavage site coding sequence of bla. All possible open reading frames (ORFs) were inserted and tested for recombination efficiency and bla activity. Efficient recombination was observed for all tested ORFs (3 for HK, 6 for ΦC31) as shown through a cointegrate formation assay. The bla gene with the embedded attB site was functional for eight of the nine constructs tested. Conclusions The HK/ΦC31 att-bla system offers a simple way to directly select recombination events, thus enhancing the use of site-specific recombination systems for carrying out precise, large-scale DNA manipulation, and adding useful tools to the genetics toolbox. We further show the power and flexibility of bla to be used as a reporter for recombination.
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Affiliation(s)
- Michael J Bland
- Unité Plasticité du Génome Bactérien, Département Génomes et Génétique, Institut Pasteur, 75015, Paris, France.,UMR3525, Centre National de la Recherche Scientifique, 75015, Paris, France
| | - Magaly Ducos-Galand
- Unité Plasticité du Génome Bactérien, Département Génomes et Génétique, Institut Pasteur, 75015, Paris, France.,UMR3525, Centre National de la Recherche Scientifique, 75015, Paris, France
| | - Marie-Eve Val
- Unité Plasticité du Génome Bactérien, Département Génomes et Génétique, Institut Pasteur, 75015, Paris, France.,UMR3525, Centre National de la Recherche Scientifique, 75015, Paris, France
| | - Didier Mazel
- Unité Plasticité du Génome Bactérien, Département Génomes et Génétique, Institut Pasteur, 75015, Paris, France. .,UMR3525, Centre National de la Recherche Scientifique, 75015, Paris, France.
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26
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Gibson SJ, Bond NJ, Milne S, Lewis A, Sheriff A, Pettman G, Pradhan R, Higazi DR, Hatton D. N-terminal or signal peptide sequence engineering prevents truncation of human monoclonal antibody light chains. Biotechnol Bioeng 2017; 114:1970-1977. [DOI: 10.1002/bit.26301] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 03/01/2017] [Accepted: 03/24/2017] [Indexed: 01/02/2023]
Affiliation(s)
- S. J. Gibson
- Department of Biopharmaceutical Development; MedImmune; Milstein Building, Granta Park Cambridge CB21 6GH United Kingdom
| | - N. J. Bond
- Department of Biopharmaceutical Development; MedImmune; Milstein Building, Granta Park Cambridge CB21 6GH United Kingdom
| | - S. Milne
- Lonza Biologics Plc; Slough Berkshire United Kingdom
| | - A. Lewis
- Department of Biopharmaceutical Development; MedImmune; Milstein Building, Granta Park Cambridge CB21 6GH United Kingdom
| | | | - G. Pettman
- Department of Biopharmaceutical Development; MedImmune; Milstein Building, Granta Park Cambridge CB21 6GH United Kingdom
| | - R. Pradhan
- Department of Biopharmaceutical Development; MedImmune; Milstein Building, Granta Park Cambridge CB21 6GH United Kingdom
| | | | - D. Hatton
- Department of Biopharmaceutical Development; MedImmune; Milstein Building, Granta Park Cambridge CB21 6GH United Kingdom
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27
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Zalucki YM, Jennings MP. 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 2017; 483:972-977. [DOI: 10.1016/j.bbrc.2017.01.044] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Accepted: 01/10/2017] [Indexed: 11/30/2022]
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28
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pMPES: A Modular Peptide Expression System for the Delivery of Antimicrobial Peptides to the Site of Gastrointestinal Infections Using Probiotics. Pharmaceuticals (Basel) 2016; 9:ph9040060. [PMID: 27782051 PMCID: PMC5198035 DOI: 10.3390/ph9040060] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 09/14/2016] [Indexed: 12/18/2022] Open
Abstract
Antimicrobial peptides are a promising alternative to traditional antibiotics, but their utility is limited by high production costs and poor bioavailability profiles. Bacterial production and delivery of antimicrobial peptides (AMPs) directly at the site of infection may offer a path for effective therapeutic application. In this study, we have developed a vector that can be used for the production and secretion of seven antimicrobial peptides from both Escherichia coli MC1061 F' and probiotic E.coli Nissle 1917. The vector pMPES (Modular Peptide Expression System) employs the Microcin V (MccV) secretion system and a powerful synthetic promoter to drive AMP production. Herein, we demonstrate the capacity of pMPES to produce inhibitory levels of MccV, Microcin L (MccL), Microcin N (McnN), Enterocin A (EntA), Enterocin P (EntP), Hiracin JM79 (HirJM79) and Enterocin B (EntB). To our knowledge, this is the first demonstration of such a broadly-applicable secretion system for AMP production. This type of modular expression system could expedite the development of sorely needed antimicrobial technologies.
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29
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Characterization of a Non-Canonical Signal Peptidase Cleavage Site in a Replication Protein from Tomato Ringspot Virus. PLoS One 2016; 11:e0162223. [PMID: 27589230 PMCID: PMC5010249 DOI: 10.1371/journal.pone.0162223] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 08/18/2016] [Indexed: 11/19/2022] Open
Abstract
The NTB-VPg polyprotein from tomato ringspot virus is an integral membrane replication protein associated with endoplasmic reticulum membranes. A signal peptidase (SPase) cleavage was previously detected in the C-terminal region of NTB-VPg downstream of a 14 amino acid (aa)-long hydrophobic region (termed TM2). However, the exact location of the cleavage site was not determined. Using in vitro translation assays, we show that the SPase cleavage site is conserved in the NTB-VPg protein from various ToRSV isolates, although the rate of cleavage varies from one isolate to another. Systematic site-directed mutagenesis of the NTB-VPg SPase cleavage sites of two ToRSV isolates allowed the identification of sequences that affect cleavage efficiency. We also present evidence that SPase cleavage in the ToRSV-Rasp2 isolate occurs within a GAAGG sequence likely after the AAG (GAAG/G). Mutation of a downstream MAAV sequence to AAAV resulted in SPase cleavage at both the natural GAAG/G and the mutated AAA/V sequences. Given that there is a distance of seven aa between the two cleavage sites, this indicates that there is flexibility in the positioning of the cleavage sites relative to the inner surface of the membrane and the SPase active site. SPase cleavage sites are typically located 3–7 aa downstream of the hydrophobic region. However, the NTB-VPg GAAG/G cleavage site is located 17 aa downstream of the TM2 hydrophobic region, highlighting unusual features of the NTB-VPg SPase cleavage site. A putative 11 aa-long amphipathic helix was identified immediately downstream of the TM2 region and five aa upstream of the GAAG/G cleavage site. Based on these results, we present an updated topology model in which the hydrophobic and amphipathic domains form a long tilted helix or a bent helix in the membrane lipid bilayer, with the downstream cleavage site(s) oriented parallel to the membrane inner surface.
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30
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Chen Q, Denard B, Lee CE, Han S, Ye JS, Ye J. Inverting the Topology of a Transmembrane Protein by Regulating the Translocation of the First Transmembrane Helix. Mol Cell 2016; 63:567-578. [PMID: 27499293 DOI: 10.1016/j.molcel.2016.06.032] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 05/13/2016] [Accepted: 06/21/2016] [Indexed: 01/07/2023]
Abstract
TM4SF20 (transmembrane 4 L6 family 20) is a polytopic membrane protein that inhibits proteolytic processing of CREB3L1 (cAMP response element-binding protein 3-like 1), a membrane-bound transcription factor that blocks cell division and activates collagen synthesis. Here we report that ceramide stimulates CREB3L1 cleavage by inverting the orientation of TM4SF20 in membranes. In the absence of ceramide, the N terminus of the first transmembrane helix of TM4SF20 is inserted into the endoplasmic reticulum (ER) lumen. This translocation requires TRAM2 (translocating chain-associated membrane protein 2), a membrane protein containing a putative ceramide-interacting domain. In the presence of ceramide, the N terminus of the first transmembrane domain of TM4SF20 is exposed to cytosol. Consequently, the membrane topology of TM4SF20 is inverted, and this form of TM4SF20 stimulates CREB3L1 cleavage. In the presence of ceramide, translocation of TM4SF20 is TRAM2-independent. We designate this mechanism-causing regulated inversion of the membrane topology as "regulated alternative translocation."
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Affiliation(s)
- Qiuyue Chen
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX 75390-9046, USA
| | - Bray Denard
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX 75390-9046, USA
| | - Ching-En Lee
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX 75390-9046, USA
| | - Sungwon Han
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX 75390-9046, USA
| | - James S Ye
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX 75390-9046, USA
| | - Jin Ye
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX 75390-9046, USA.
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31
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Ting YT, Harris PWR, Batot G, Brimble MA, Baker EN, Young PG. Peptide binding to a bacterial signal peptidase visualized by peptide tethering and carrier-driven crystallization. IUCRJ 2016; 3:10-9. [PMID: 26870377 PMCID: PMC4704075 DOI: 10.1107/s2052252515019971] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 10/22/2015] [Indexed: 05/22/2023]
Abstract
Bacterial type I signal peptidases (SPases) are membrane-anchored serine proteases that process the signal peptides of proteins exported via the Sec and Tat secretion systems. Despite their crucial importance for bacterial virulence and their attractiveness as drug targets, only one such enzyme, LepB from Escherichia coli, has been structurally characterized, and the transient nature of peptide binding has stymied attempts to directly visualize SPase-substrate complexes. Here, the crystal structure of SpsB, the type I signal peptidase from the Gram-positive pathogen Staphylococcus aureus, is reported, and a peptide-tethering strategy that exploits the use of carrier-driven crystallization is described. This enabled the determination of the crystal structures of three SpsB-peptide complexes, both with cleavable substrates and with an inhibitory peptide. SpsB-peptide interactions in these complexes are almost exclusively limited to the canonical signal-peptide motif Ala-X-Ala, for which clear specificity pockets are found. Minimal contacts are made outside this core, with the variable side chains of the peptides accommodated in shallow grooves or exposed faces. These results illustrate how high fidelity is retained despite broad sequence diversity, in a process that is vital for cell survival.
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Affiliation(s)
- Yi Tian Ting
- School of Biological Sciences, The University of Auckland, Auckland 1142, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland 1142, New Zealand
| | - Paul W. R. Harris
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland 1142, New Zealand
- School of Chemical Sciences, The University of Auckland, Auckland 1142, New Zealand
| | - Gaelle Batot
- School of Biological Sciences, The University of Auckland, Auckland 1142, New Zealand
| | - Margaret A. Brimble
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland 1142, New Zealand
- School of Chemical Sciences, The University of Auckland, Auckland 1142, New Zealand
| | - Edward N. Baker
- School of Biological Sciences, The University of Auckland, Auckland 1142, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland 1142, New Zealand
| | - Paul G. Young
- School of Biological Sciences, The University of Auckland, Auckland 1142, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland 1142, New Zealand
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32
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Xiang DF, Bigley AN, Ren Z, Xue H, Hull KG, Romo D, Raushel FM. Interrogation of the Substrate Profile and Catalytic Properties of the Phosphotriesterase from Sphingobium sp. Strain TCM1: An Enzyme Capable of Hydrolyzing Organophosphate Flame Retardants and Plasticizers. Biochemistry 2015; 54:7539-49. [DOI: 10.1021/acs.biochem.5b01144] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Dao Feng Xiang
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Andrew N. Bigley
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Zhongjie Ren
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77843, United States
| | - Haoran Xue
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Kenneth G. Hull
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Daniel Romo
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Frank M. Raushel
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77843, United States
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Sakurai T, Sakurai A, Vaisman BL, Amar MJ, Liu C, Gordon SM, Drake SK, Pryor M, Sampson ML, Yang L, Freeman LA, Remaley AT. Creation of Apolipoprotein C-II (ApoC-II) Mutant Mice and Correction of Their Hypertriglyceridemia with an ApoC-II Mimetic Peptide. J Pharmacol Exp Ther 2015; 356:341-53. [PMID: 26574515 DOI: 10.1124/jpet.115.229740] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 11/11/2015] [Indexed: 12/31/2022] Open
Abstract
Apolipoprotein C-II (apoC-II) is a cofactor for lipoprotein lipase, a plasma enzyme that hydrolyzes triglycerides (TGs). ApoC-II deficiency in humans results in hypertriglyceridemia. We used zinc finger nucleases to create Apoc2 mutant mice to investigate the use of C-II-a, a short apoC-II mimetic peptide, as a therapy for apoC-II deficiency. Mutant mice produced a form of apoC-II with an uncleaved signal peptide that preferentially binds high-density lipoproteins (HDLs) due to a 3-amino acid deletion at the signal peptide cleavage site. Homozygous Apoc2 mutant mice had increased plasma TG (757.5 ± 281.2 mg/dl) and low HDL cholesterol (31.4 ± 14.7 mg/dl) compared with wild-type mice (TG, 55.9 ± 13.3 mg/dl; HDL cholesterol, 55.9 ± 14.3 mg/dl). TGs were found in light (density < 1.063 g/ml) lipoproteins in the size range of very-low-density lipoprotein and chylomicron remnants (40-200 nm). Intravenous injection of C-II-a (0.2, 1, and 5 μmol/kg) reduced plasma TG in a dose-dependent manner, with a maximum decrease of 90% occurring 30 minutes after the high dose. Plasma TG did not return to baseline until 48 hours later. Similar results were found with subcutaneous or intramuscular injections. Plasma half-life of C-II-a is 1.33 ± 0.72 hours, indicating that C-II-a only acutely activates lipolysis, and the sustained TG reduction is due to the relatively slow rate of new TG-rich lipoprotein synthesis. In summary, we describe a novel mouse model of apoC-II deficiency and show that an apoC-II mimetic peptide can reverse the hypertriglyceridemia in these mice, and thus could be a potential new therapy for apoC-II deficiency.
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Affiliation(s)
- Toshihiro Sakurai
- Lipoprotein Metabolism Section, Cardio-Pulmonary Branch, National Heart, Lung, and Blood Institute (T.S., A.S., B.L.V., M.J.A., C.L., S.M.G., M.P., L.A.F., A.T.R.), Transgenic Core Facility, National Heart, Lung, and Blood Institute (C.L.), Department of Laboratory Medicine, Clinical Center (M.L.S., A.T.R.), Critical Care Medicine Department, Clinical Center (S.K.D.), and Laboratory of Obesity and Metabolic Diseases, National Heart, Lung, and Blood Institute (L.Y.), National Institutes of Health, Bethesda, Maryland
| | - Akiko Sakurai
- Lipoprotein Metabolism Section, Cardio-Pulmonary Branch, National Heart, Lung, and Blood Institute (T.S., A.S., B.L.V., M.J.A., C.L., S.M.G., M.P., L.A.F., A.T.R.), Transgenic Core Facility, National Heart, Lung, and Blood Institute (C.L.), Department of Laboratory Medicine, Clinical Center (M.L.S., A.T.R.), Critical Care Medicine Department, Clinical Center (S.K.D.), and Laboratory of Obesity and Metabolic Diseases, National Heart, Lung, and Blood Institute (L.Y.), National Institutes of Health, Bethesda, Maryland
| | - Boris L Vaisman
- Lipoprotein Metabolism Section, Cardio-Pulmonary Branch, National Heart, Lung, and Blood Institute (T.S., A.S., B.L.V., M.J.A., C.L., S.M.G., M.P., L.A.F., A.T.R.), Transgenic Core Facility, National Heart, Lung, and Blood Institute (C.L.), Department of Laboratory Medicine, Clinical Center (M.L.S., A.T.R.), Critical Care Medicine Department, Clinical Center (S.K.D.), and Laboratory of Obesity and Metabolic Diseases, National Heart, Lung, and Blood Institute (L.Y.), National Institutes of Health, Bethesda, Maryland
| | - Marcelo J Amar
- Lipoprotein Metabolism Section, Cardio-Pulmonary Branch, National Heart, Lung, and Blood Institute (T.S., A.S., B.L.V., M.J.A., C.L., S.M.G., M.P., L.A.F., A.T.R.), Transgenic Core Facility, National Heart, Lung, and Blood Institute (C.L.), Department of Laboratory Medicine, Clinical Center (M.L.S., A.T.R.), Critical Care Medicine Department, Clinical Center (S.K.D.), and Laboratory of Obesity and Metabolic Diseases, National Heart, Lung, and Blood Institute (L.Y.), National Institutes of Health, Bethesda, Maryland
| | - Chengyu Liu
- Lipoprotein Metabolism Section, Cardio-Pulmonary Branch, National Heart, Lung, and Blood Institute (T.S., A.S., B.L.V., M.J.A., C.L., S.M.G., M.P., L.A.F., A.T.R.), Transgenic Core Facility, National Heart, Lung, and Blood Institute (C.L.), Department of Laboratory Medicine, Clinical Center (M.L.S., A.T.R.), Critical Care Medicine Department, Clinical Center (S.K.D.), and Laboratory of Obesity and Metabolic Diseases, National Heart, Lung, and Blood Institute (L.Y.), National Institutes of Health, Bethesda, Maryland
| | - Scott M Gordon
- Lipoprotein Metabolism Section, Cardio-Pulmonary Branch, National Heart, Lung, and Blood Institute (T.S., A.S., B.L.V., M.J.A., C.L., S.M.G., M.P., L.A.F., A.T.R.), Transgenic Core Facility, National Heart, Lung, and Blood Institute (C.L.), Department of Laboratory Medicine, Clinical Center (M.L.S., A.T.R.), Critical Care Medicine Department, Clinical Center (S.K.D.), and Laboratory of Obesity and Metabolic Diseases, National Heart, Lung, and Blood Institute (L.Y.), National Institutes of Health, Bethesda, Maryland
| | - Steven K Drake
- Lipoprotein Metabolism Section, Cardio-Pulmonary Branch, National Heart, Lung, and Blood Institute (T.S., A.S., B.L.V., M.J.A., C.L., S.M.G., M.P., L.A.F., A.T.R.), Transgenic Core Facility, National Heart, Lung, and Blood Institute (C.L.), Department of Laboratory Medicine, Clinical Center (M.L.S., A.T.R.), Critical Care Medicine Department, Clinical Center (S.K.D.), and Laboratory of Obesity and Metabolic Diseases, National Heart, Lung, and Blood Institute (L.Y.), National Institutes of Health, Bethesda, Maryland
| | - Milton Pryor
- Lipoprotein Metabolism Section, Cardio-Pulmonary Branch, National Heart, Lung, and Blood Institute (T.S., A.S., B.L.V., M.J.A., C.L., S.M.G., M.P., L.A.F., A.T.R.), Transgenic Core Facility, National Heart, Lung, and Blood Institute (C.L.), Department of Laboratory Medicine, Clinical Center (M.L.S., A.T.R.), Critical Care Medicine Department, Clinical Center (S.K.D.), and Laboratory of Obesity and Metabolic Diseases, National Heart, Lung, and Blood Institute (L.Y.), National Institutes of Health, Bethesda, Maryland
| | - Maureen L Sampson
- Lipoprotein Metabolism Section, Cardio-Pulmonary Branch, National Heart, Lung, and Blood Institute (T.S., A.S., B.L.V., M.J.A., C.L., S.M.G., M.P., L.A.F., A.T.R.), Transgenic Core Facility, National Heart, Lung, and Blood Institute (C.L.), Department of Laboratory Medicine, Clinical Center (M.L.S., A.T.R.), Critical Care Medicine Department, Clinical Center (S.K.D.), and Laboratory of Obesity and Metabolic Diseases, National Heart, Lung, and Blood Institute (L.Y.), National Institutes of Health, Bethesda, Maryland
| | - Ling Yang
- Lipoprotein Metabolism Section, Cardio-Pulmonary Branch, National Heart, Lung, and Blood Institute (T.S., A.S., B.L.V., M.J.A., C.L., S.M.G., M.P., L.A.F., A.T.R.), Transgenic Core Facility, National Heart, Lung, and Blood Institute (C.L.), Department of Laboratory Medicine, Clinical Center (M.L.S., A.T.R.), Critical Care Medicine Department, Clinical Center (S.K.D.), and Laboratory of Obesity and Metabolic Diseases, National Heart, Lung, and Blood Institute (L.Y.), National Institutes of Health, Bethesda, Maryland
| | - Lita A Freeman
- Lipoprotein Metabolism Section, Cardio-Pulmonary Branch, National Heart, Lung, and Blood Institute (T.S., A.S., B.L.V., M.J.A., C.L., S.M.G., M.P., L.A.F., A.T.R.), Transgenic Core Facility, National Heart, Lung, and Blood Institute (C.L.), Department of Laboratory Medicine, Clinical Center (M.L.S., A.T.R.), Critical Care Medicine Department, Clinical Center (S.K.D.), and Laboratory of Obesity and Metabolic Diseases, National Heart, Lung, and Blood Institute (L.Y.), National Institutes of Health, Bethesda, Maryland
| | - Alan T Remaley
- Lipoprotein Metabolism Section, Cardio-Pulmonary Branch, National Heart, Lung, and Blood Institute (T.S., A.S., B.L.V., M.J.A., C.L., S.M.G., M.P., L.A.F., A.T.R.), Transgenic Core Facility, National Heart, Lung, and Blood Institute (C.L.), Department of Laboratory Medicine, Clinical Center (M.L.S., A.T.R.), Critical Care Medicine Department, Clinical Center (S.K.D.), and Laboratory of Obesity and Metabolic Diseases, National Heart, Lung, and Blood Institute (L.Y.), National Institutes of Health, Bethesda, Maryland
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Cui J, Chen W, Sun J, Guo H, Madley R, Xiong Y, Pan X, Wang H, Tai AW, Weiss MA, Arvan P, Liu M. Competitive Inhibition of the Endoplasmic Reticulum Signal Peptidase by Non-cleavable Mutant Preprotein Cargos. J Biol Chem 2015; 290:28131-28140. [PMID: 26446786 DOI: 10.1074/jbc.m115.692350] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Indexed: 12/30/2022] Open
Abstract
Upon translocation across the endoplasmic reticulum (ER) membrane, secretory proteins are proteolytically processed to remove their signal peptide by signal peptidase (SPase). This process is critical for subsequent folding, intracellular trafficking, and maturation of secretory proteins. Prokaryotic SPase has been shown to be a promising antibiotic target. In contrast, to date, no eukaryotic SPase inhibitors have been reported. Here we report that introducing a proline immediately following the natural signal peptide cleavage site not only blocks preprotein cleavage but also, in trans, impairs the processing and maturation of co-expressed preproteins in the ER. Specifically, we find that a variant preproinsulin, pPI-F25P, is translocated across the ER membrane, where it binds to the catalytic SPase subunit SEC11A, inhibiting SPase activity in a dose-dependent manner. Similar findings were obtained with an analogous variant of preproparathyroid hormone, demonstrating that inhibition of the SPase does not depend strictly on the sequence or structure of the downstream mature protein. We further show that inhibiting SPase in the ER impairs intracellular processing of viral polypeptides and their subsequent maturation. These observations suggest that eukaryotic SPases (including the human ortholog) are, in principle, suitable therapeutic targets for antiviral drug design.
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Affiliation(s)
- Jingqiu Cui
- Department of Endocrinology and Metabolism, Tianjin Medical University General Hospital, Tianjin 300052, China,; Division of Metabolism, Endocrinology, and Diabetes, University of Michigan Medical School, Ann Arbor, Michigan 48105
| | - Wei Chen
- Division of Metabolism, Endocrinology, and Diabetes, University of Michigan Medical School, Ann Arbor, Michigan 48105,; Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China
| | - Jinhong Sun
- Division of Metabolism, Endocrinology, and Diabetes, University of Michigan Medical School, Ann Arbor, Michigan 48105
| | - Huan Guo
- Division of Metabolism, Endocrinology, and Diabetes, University of Michigan Medical School, Ann Arbor, Michigan 48105
| | - Rachel Madley
- Division of Metabolism, Endocrinology, and Diabetes, University of Michigan Medical School, Ann Arbor, Michigan 48105
| | - Yi Xiong
- Division of Metabolism, Endocrinology, and Diabetes, University of Michigan Medical School, Ann Arbor, Michigan 48105
| | - Xingyi Pan
- Division of Metabolism, Endocrinology, and Diabetes, University of Michigan Medical School, Ann Arbor, Michigan 48105
| | - Hongliang Wang
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48109
| | - Andrew W Tai
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48109
| | - Michael A Weiss
- Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio 44106.
| | - Peter Arvan
- Division of Metabolism, Endocrinology, and Diabetes, University of Michigan Medical School, Ann Arbor, Michigan 48105
| | - Ming Liu
- Department of Endocrinology and Metabolism, Tianjin Medical University General Hospital, Tianjin 300052, China,; Division of Metabolism, Endocrinology, and Diabetes, University of Michigan Medical School, Ann Arbor, Michigan 48105
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Dong Z, Zhang J, Du G, Chen J, Li H, Lee B. Periplasmic Export of Bile Salt Hydrolase in Escherichia coli by the Twin-Arginine Signal Peptides. Appl Biochem Biotechnol 2015. [PMID: 26198023 DOI: 10.1007/s12010-015-1755-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Bile salt hydrolase (BSH, EC 3.5.1.24) is considered as an ideal way with lower cost and less side effects to release the risk of coronary heart disease caused by hypercholesterolemia. As bile salt hydrolase from Lactobacillus plantarum BBE7 could not be efficiently exported by PelB signal peptide of the general secretory (Sec) pathway, three twin-arginine signal peptides from twin-arginine translocation (Tat) pathway were synthesized, fused with bsh gene, inserted into expression vectors pET-20b(+) and pET-22b(+), and transformed into four different Escherichia coli hosts, respectively. Among the 24 recombinant bacteria obtained, E. coli BL21 (DE3) pLysS (pET-20b(+)-dmsA-bsh) showed the highest BSH activity in periplasmic fraction, which was further increased to 1.21 ± 0.03 U/mL by orthogonal experimental design. And, signal peptide dimethyl sulfoxide reductase subunit DmsA (DMSA) had the best activity of exported BSH. More importantly, the presence of BSH in the periplasm had proven to be caused by the export rather than cell leakage. For the first time, we report the periplasmic expression of BSH by signal peptides from the Tat pathway. This will lay a solid foundation for the purification and biochemical characterization of BSH from the supernatant, and strategies adopted here could be used for the periplasmic expression of other proteins in E. coli.
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Affiliation(s)
- Zixing Dong
- College of Chemical Engineering and Material Science, Tianjin University of Science & Technology, Tianjin, 300457, China
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Mathew J, Jagadeesh SM, Bhat M, Udhaya Kumar S, Thiyagarajan S, Srinivasan S. Mutations in ARSB in MPS VI patients in India. Mol Genet Metab Rep 2015; 4:53-61. [PMID: 26937411 PMCID: PMC4750586 DOI: 10.1016/j.ymgmr.2015.06.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 06/08/2015] [Accepted: 06/08/2015] [Indexed: 12/31/2022] Open
Abstract
Mucopolysaccharidosis VI (MPS VI) is an autosomal recessive inborn error of metabolism caused by mutations in the arylsulfatase B gene (ARSB) and consequent deficient activity of ARSB, a lysosomal enzyme. We present here the results of a study undertaken to identify the mutations in ARSB in MPS VI patients in India. Around 160 ARSB mutations, of which just 4 are from India, have been reported in the literature. Our study covered nine MPS VI patients from eight families. Both familial mutations were found in seven families, and only one mutation was found in one family. Seven mutations were found - four novel (p.G38_G40del3, p.C91R, p.L98R and p.R315P), two previously reported from India (p.D53N and p.W450C), and one reported from outside India (p.R160Q). One mutation, p.W450C, was present in two families, and the other six mutations were present in one family each. Analysis of the molecular structure of the enzyme revealed that most of these mutations either cause loss of an active site residue or destabilize the structure of the enzyme. The only previous study on mutations in ARSB in Indian MPS VI patients, by Kantaputra et al. 2014 [1], reported four novel mutations of which two (p.D53N and p.W450C) were found in our study as well. Till date, nine mutations have been reported from India, through our study and the Kantaputra study. Eight out of these nine mutations have been found only in India. This suggests that the population studied by us might have its own typical set of mutations, with other populations equally likely to have their own set of mutations.
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Key Words
- ARSB, arylsulfatase B
- Active site
- Arylsulfatase B (ARSB)
- ERT, enzyme replacement therapy
- GAG, glycosaminoglycan
- GALNS, N-acetyl galactosamine 6-sulfatase
- HGMD, Human Gene Mutation Database
- HSCT, hematopoietic stem cell transplantation
- Inborn error of metabolism (IEM)
- India
- LSD, lysosomal storage disorder
- Lysosomal enzyme
- Lysosomal storage disorder (LSD)
- MPS, mucopolysaccharidosis
- Maroteaux–Lamy syndrome
- Mucopolysaccharidosis VI (MPS VI)
- Mutations
- PCT, pharmacological chaperone therapy
- VUS, variants of unknown significance
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Affiliation(s)
- Juby Mathew
- Centre for Human Genetics (CHG), Bangalore, India
| | - Sujatha M Jagadeesh
- Department of Clinical Genetics, Fetal Care Research Foundation (FCRF), Chennai, India
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Guan ZB, Shui Y, Song CM, Zhang N, Cai YJ, Liao XR. Efficient secretory production of CotA-laccase and its application in the decolorization and detoxification of industrial textile wastewater. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:9515-9523. [PMID: 25847445 DOI: 10.1007/s11356-015-4426-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 03/20/2015] [Indexed: 06/04/2023]
Abstract
Fungal laccases are typically unstable at high pH and temperature conditions, which limit their application in the decolorization of textile wastewater. By contrast, the highly stable bacterial laccases can function within a wider pH range and at high temperatures, thus have significant potential in treatment for textile wastewater. In our previous work, a thermo-alkali-stable CotA-laccase gene was cloned from Bacillus pumilus W3 and overexpressed in Escherichia coli. In this study, the robust CotA-laccase achieved efficient secretory expression in Bacillus subtilis WB600 by screening a suitable signal peptide. A maximum CotA-laccase yield of 373.1 U/mL was obtained at optimum culture conditions in a 3-L fermentor. Furthermore, the decolorization and detoxification of textile industry effluent by the purified recombinant CotA-laccase in the presence and absence of redox mediators were investigated. Among the potential mediators that enhanced effluent decolorization, acetosyringone (ACS) was the most effective. The toxicity of the CotA-laccase-ACS-treated effluent was greatly reduced compared with that of the crude effluent. To the best of our knowledge, this study is the first to report on the heterologous expression of CotA-laccase in B. subtilis. The recombinant strain B. subtilis WB600-5 has a great potential in the industrial production of this bacterial enzyme, and the CotA-laccase-ACS system is a promising candidate for the biological treatment of industrial textile effluents.
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Affiliation(s)
- Zheng-Bing Guan
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, People's Republic of China,
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Blitvich BJ, Firth AE. Insect-specific flaviviruses: a systematic review of their discovery, host range, mode of transmission, superinfection exclusion potential and genomic organization. Viruses 2015; 7:1927-59. [PMID: 25866904 PMCID: PMC4411683 DOI: 10.3390/v7041927] [Citation(s) in RCA: 226] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 03/30/2015] [Accepted: 04/08/2015] [Indexed: 12/11/2022] Open
Abstract
There has been a dramatic increase in the number of insect-specific flaviviruses (ISFs) discovered in the last decade. Historically, these viruses have generated limited interest due to their inability to infect vertebrate cells. This viewpoint has changed in recent years because some ISFs have been shown to enhance or suppress the replication of medically important flaviviruses in co-infected mosquito cells. Additionally, comparative studies between ISFs and medically important flaviviruses can provide a unique perspective as to why some flaviviruses possess the ability to infect and cause devastating disease in humans while others do not. ISFs have been isolated exclusively from mosquitoes in nature but the detection of ISF-like sequences in sandflies and chironomids indicates that they may also infect other dipterans. ISFs can be divided into two distinct phylogenetic groups. The first group currently consists of approximately 12 viruses and includes cell fusing agent virus, Kamiti River virus and Culex flavivirus. These viruses are phylogenetically distinct from all other known flaviviruses. The second group, which is apparently not monophyletic, currently consists of nine viruses and includes Chaoyang virus, Nounané virus and Lammi virus. These viruses phylogenetically affiliate with mosquito/vertebrate flaviviruses despite their apparent insect-restricted phenotype. This article provides a review of the discovery, host range, mode of transmission, superinfection exclusion ability and genomic organization of ISFs. This article also attempts to clarify the ISF nomenclature because some of these viruses have been assigned more than one name due to their simultaneous discoveries by independent research groups.
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Affiliation(s)
- Bradley J Blitvich
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA.
| | - Andrew E Firth
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK.
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Vallesi A, Alimenti C, Federici S, Di Giuseppe G, Dini F, Guella G, Luporini P. Evidence for gene duplication and allelic codominance (not hierarchical dominance) at the mating-type locus of the ciliate, Euplotes crassus. J Eukaryot Microbiol 2014; 61:620-9. [PMID: 25040318 DOI: 10.1111/jeu.12140] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Revised: 03/25/2014] [Accepted: 05/03/2014] [Indexed: 11/30/2022]
Abstract
The high-multiple mating system of Euplotes crassus is known to be controlled by multiple alleles segregating at a single locus and manifesting relationships of hierarchical dominance, so that heterozygous cells would produce a single mating-type substance (pheromone). In strain L-2D, now known to be homozygous at the mating-type locus, we previously identified two pheromones (Ec-α and Ec-1) characterized by significant variations in their amino acid sequences and structure of their macronuclear coding genes. In this study, pheromones and macronuclear coding genes have been analyzed in strain POR-73 characterized by a heterozygous genotype and strong mating compatibility with L-2D strain. It was found that POR-73 cells contain three distinct pheromone coding genes and, accordingly, secrete three distinct pheromones. One pheromone revealed structural identity in amino acid sequence and macronuclear coding gene to the Ec-α pheromone of L-2D cells. The other two pheromones were shown to be new and were designated Ec-2 and Ec-3 to denote their structural homology with the Ec-1 pheromone of L-2D cells. We interpreted these results as evidence of a phenomenon of gene duplication at the E. crassus mating-type locus, and lack of hierarchical dominance in the expression of the macronuclear pheromone genes in cells with heterozygous genotypes.
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Affiliation(s)
- Adriana Vallesi
- Laboratory of Eukaryotic Microbiology and Animal Biology, University of Camerino, 62032, Camerino, MC, Italy
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Functional rectification of the newly described African henipavirus fusion glycoprotein (Gh-M74a). J Virol 2014; 88:5171-6. [PMID: 24522929 DOI: 10.1128/jvi.03655-13] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Recent evidence identified multiple Henipavirus species in Africa distinct from those in Southeast Asia and Australia. The reported fusion glycoprotein (F) sequence of the African Gh-M74a strain (GhV-F) is likely incorrect: a single base pair deletion near the N terminus results in multiple aberrancies. Rectifying this by adding single nucleotide insertions results in a GhV-F that now possesses a signal peptide, is efficiently cell surface expressed, exhibits syncytium formation when coexpressed with GhV-G protein, and mediates pseudotyped viral particle entry.
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Dhanaraj P, James JV, Michael PG, Muthiah I. SIGLOCPRED: an algorithm to predict bacterial signal peptides and OMPS. Bioinformation 2012; 8:970-3. [PMID: 23275689 PMCID: PMC3524949 DOI: 10.6026/97320630008970] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 09/09/2012] [Indexed: 11/23/2022] Open
Abstract
There is a growing interest in Biological investigation to determine the location of proteins, to identify new potentially accessible drug targets. Signal peptide directs the transport of the protein to its location. Bacterial OMPs are essential for their survival in the host organism. SIGLOCPRED a signal peptide predictor for the bacterial proteins as well as OMP prediction has been developed. The signal peptide prediction is done based on the influence of the flanking residues on the signal peptide cleavage. A dataset of proteins with confirmed outer membrane location has being created, and the probable OMP polypeptide sequence is predicted. Since the algorithm uses confirmed datasets the prediction is more reliable and efficient. SIGLOCPRED is as efficient as many of the existing signal peptide predictors and can also predict OMPs in addition.
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Affiliation(s)
- Premnath Dhanaraj
- School of Biotechnology and Health Science, Karunya University, INDIA
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Wang SK, Chan HC, Rajderkar S, Milkovich RN, Uston KA, Kim JW, Simmer JP, Hu JCC. Enamel malformations associated with a defined dentin sialophosphoprotein mutation in two families. Eur J Oral Sci 2011; 119 Suppl 1:158-67. [PMID: 22243242 PMCID: PMC3266624 DOI: 10.1111/j.1600-0722.2011.00874.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Dentin sialophosphoprotein (DSPP) mutations cause dentin dysplasia type II (DD-II) and dentinogenesis imperfecta types II and III (DGI-II and DGI-III, respectively). We identified two kindreds with DGI-II who exhibited vertical bands of hypoplastic enamel. Both families had a previously reported DSPP mutation that segregated with the disease phenotype. Oral photographs and dental radiographs of four affected and one unaffected participant in one family and of the proband in the second family were used to document the dental phenotypes. We aligned the 33 unique allelic DSPP sequences showing variable patterns of insertions and deletions (indels), generated a merged dentin phosphoprotein (DPP) sequence that includes sequences from all DSPP length haplotypes, and mapped the known DSPP mutations in this context. Analyses of the DSPP sequence changes and their probable effects on protein expression, as well as published findings of the dental phenotype in Dspp null mice, support the hypothesis that all DSPP mutations cause pathology through dominant-negative effects. Noting that Dspp is transiently expressed by mouse pre-ameloblasts during formation of the dentino-enamel junction, we hypothesize that DSPP dominant-negative effects potentially cause cellular pathology in pre-ameloblasts that, in turn, causes enamel defects. We conclude that enamel defects can be part of the dental phenotype caused by DSPP mutations, although DSPP is not critical for dental enamel formation.
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Affiliation(s)
- Shih-Kai Wang
- Department of Biologic and Materials Sciences, University of Michigan School of Dentistry, 1210 Eisenhower Place, Ann Arbor, MI, USA 48108
- Oral Health Sciences program, University of Michigan School of Dentistry; 1011 North University, Ann Arbor, MI, USA 48109
| | - Hui-Chen Chan
- Department of Biologic and Materials Sciences, University of Michigan School of Dentistry, 1210 Eisenhower Place, Ann Arbor, MI, USA 48108
| | - Sudha Rajderkar
- Oral Health Sciences program, University of Michigan School of Dentistry; 1011 North University, Ann Arbor, MI, USA 48109
| | - Rachel N. Milkovich
- Department of Biologic and Materials Sciences, University of Michigan School of Dentistry, 1210 Eisenhower Place, Ann Arbor, MI, USA 48108
| | - Karen A. Uston
- Department of Orthodontics and Pediatric Dentistry, University of Michigan School of Dentistry, 1011 North University, Ann Arbor, MI, USA 48109
| | - Jung-Wook Kim
- Department of Pediatric Dentistry & Dental Research Institute, School of Dentistry, Seoul National University, 275-1 Yongon-dong, Chongno-gu, Seoul 110-768, Korea
| | - James P. Simmer
- Department of Biologic and Materials Sciences, University of Michigan School of Dentistry, 1210 Eisenhower Place, Ann Arbor, MI, USA 48108
| | - Jan C-C. Hu
- Department of Biologic and Materials Sciences, University of Michigan School of Dentistry, 1210 Eisenhower Place, Ann Arbor, MI, USA 48108
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Auclair SM, Bhanu MK, Kendall DA. Signal peptidase I: cleaving the way to mature proteins. Protein Sci 2011; 21:13-25. [PMID: 22031009 DOI: 10.1002/pro.757] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2011] [Revised: 10/12/2011] [Accepted: 10/17/2011] [Indexed: 11/07/2022]
Abstract
Signal peptidase I (SPase I) is critical for the release of translocated preproteins from the membrane as they are transported from a cytoplasmic site of synthesis to extracytoplasmic locations. These proteins are synthesized with an amino-terminal extension, the signal sequence, which directs the preprotein to the Sec- or Tat-translocation pathway. Recent evidence indicates that the SPase I cleaves preproteins as they emerge from either pathway, though the steps involved are unclear. Now that the structure of many translocation pathway components has been elucidated, it is critical to determine how these components work in concert to support protein translocation and cleavage. Molecular modeling and NMR studies have provided insight on how the preprotein docks on SPase I in preparation for cleavage. This is a key area for future work since SPase I enzymes in a variety of species have now been identified and the inhibition of these enzymes by antibiotics is being pursued. The eubacterial SPase I is essential for cell viability and belongs to a unique group of serine endoproteases which utilize a Ser-Lys catalytic dyad instead of the prototypical Ser-His-Asp triad used by eukaryotes. As such, SPase I is a desirable antimicrobial target. Advances in our understanding of how the preprotein interfaces with SPase I during the final stages of translocation will facilitate future development of inhibitors that display a high efficacy against SPase I function.
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Affiliation(s)
- Sarah M Auclair
- Department of Pharmaceutical Sciences, The University of Connecticut, Storrs, CT 06269, USA
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Alimenti C, Vallesi A, Federici S, di Giuseppe G, Fernando D, Carratore V, Luporini P. Isolation and structural characterization of two water-borne pheromones from Euplotes crassus, a ciliate commonly known to carry membrane-bound pheromones. J Eukaryot Microbiol 2011; 58:234-41. [PMID: 21414056 DOI: 10.1111/j.1550-7408.2011.00535.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ciliates comprise species synthesizing water-diffusible mating type factors or pheromones and species synthesizing insoluble, cell membrane-bound pheromones. Euplotes crassus has traditionally been placed in the latter group. In contrast with this notion, we found that E. crassus is a constitutive pheromone-secreting ciliate, like other Euplotes species. From cell-free filtrate preparations of the E. crassus strain L-2D, we isolated two distinct pheromones, designated as Ec-α and Ec-1, and determined their complete amino acid sequences by combined chemical and genetic approaches. The Ec-α pheromone sequence extends for 56 amino acid residues with six cysteines and shows a molecular mass of 6,183 Da, while the Ec-1 pheromone sequence extends for 45 amino acid residues with 10 cysteines and shows a molecular mass of 4,840 Da. Marked structural differences distinguish the full-length Ec-α and Ec-1 coding sequences, which have been cloned and characterized from the transcriptionally active macronuclear genome. They were taken as clear indication that the Ec-α and Ec-1 pheromones are specified by genes that are not allelic, but likely derived from a duplicated genetic locus of the transcriptionally silent micronuclear genome.
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Affiliation(s)
- Claudio Alimenti
- Dipartimento di Scienze Ambientali e Naturali, University of Camerino, 62032 Camerino (MC), Italy
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Broad-spectrum antibiotic activity of the arylomycin natural products is masked by natural target mutations. ACTA ACUST UNITED AC 2011; 17:1223-31. [PMID: 21095572 DOI: 10.1016/j.chembiol.2010.09.009] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2010] [Revised: 09/09/2010] [Accepted: 09/13/2010] [Indexed: 11/23/2022]
Abstract
Novel classes of broad-spectrum antibiotics are needed to treat multidrug-resistant pathogens. The arylomycin class of natural products inhibits a promising antimicrobial target, type I signal peptidase (SPase), but upon initial characterization appeared to lack whole-cell activity against most pathogens. Here, we show that Staphylococcus epidermidis, which is sensitive to the arylomycins, evolves resistance via mutations in SPase and that analogous mutations are responsible for the natural resistance of Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa. We identify diverse bacteria lacking these mutations and demonstrate that most are sensitive to the arylomycins. The results illustrate that the arylomycins have a broad-spectrum of activity and are viable candidates for development into therapeutics. The results also raise the possibility that naturally occurring resistance may have masked other natural product scaffolds that might be developed into therapeutics.
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Abstract
Bacterial protein secretion is a highly orchestrated process that is essential for infection and virulence. Despite extensive efforts to predict or experimentally detect proteins that are secreted, the characterization of the bacterial secretome has remained challenging. A central event in protein secretion is the type I signal peptidase (SPase)-mediated cleavage of the N-terminal signal peptide that targets a protein for secretion via the general secretory pathway, and the arylomycins are a class of natural products that inhibit SPase, suggesting that they may be useful chemical biology tools for characterizing the secretome. Here, using an arylomycin derivative, along with two-dimensional gel electrophoresis and liquid chromatography-tandem mass spectrometry (LC-MS/MS), we identify 11 proteins whose secretion from stationary-phase Staphylococcus epidermidis is dependent on SPase activity, 9 of which are predicted to be translated with canonical N-terminal signal peptides. In addition, we find that the presence of extracellular domains of lipoteichoic acid synthase (LtaS) and the β-lactam response sensor BlaR1 in the medium is dependent on SPase activity, suggesting that they are cleaved at noncanonical sites within the protein. In all, the data define the proteins whose stationary-phase secretion depends on SPase and also suggest that the arylomycins should be valuable chemical biology tools for the study of protein secretion in a wide variety of different bacteria.
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Optimization of protease secretion in Bacillus subtilis and Bacillus licheniformis by screening of homologous and heterologous signal peptides. Appl Environ Microbiol 2010; 76:6370-6. [PMID: 20709850 DOI: 10.1128/aem.01146-10] [Citation(s) in RCA: 119] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacillus subtilis and Bacillus licheniformis are widely used for the large-scale industrial production of proteins. These strains can efficiently secrete proteins into the culture medium using the general secretion (Sec) pathway. A characteristic feature of all secreted proteins is their N-terminal signal peptides, which are recognized by the secretion machinery. Here, we have studied the production of an industrially important secreted protease, namely, subtilisin BPN' from Bacillus amyloliquefaciens. One hundred seventy-three signal peptides originating from B. subtilis and 220 signal peptides from the B. licheniformis type strain were fused to this secretion target and expressed in B. subtilis, and the resulting library was analyzed by high-throughput screening for extracellular proteolytic activity. We have identified a number of signal peptides originating from both organisms which produced significantly increased yield of the secreted protease. Interestingly, we observed that levels of extracellular protease were improved not only in B. subtilis, which was used as the screening host, but also in two different B. licheniformis strains. To date, it is impossible to predict which signal peptide will result in better secretion and thus an improved yield of a given extracellular target protein. Our data show that screening a library consisting of homologous and heterologous signal peptides fused to a target protein can identify more-effective signal peptides, resulting in improved protein export not only in the original screening host but also in different production strains.
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Bintintan I, Meyers G. A new type of signal peptidase cleavage site identified in an RNA virus polyprotein. J Biol Chem 2010; 285:8572-84. [PMID: 20093364 DOI: 10.1074/jbc.m109.083394] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Pestiviruses, a group of enveloped positive strand RNA viruses belonging to the family Flaviviridae, express their genes via a polyprotein that is subsequently processed by proteases. The structural protein region contains typical signal peptidase cleavage sites. Only the site at the C terminus of the glycoprotein E(rns) is different because it does not contain a hydrophobic transmembrane region but an amphipathic helix functioning as the E(rns) membrane anchor. Despite the absence of a hydrophobic region, the site between the C terminus of E(rns) and E1, the protein located downstream in the polyprotein, is cleaved by signal peptidase, as demonstrated by mutagenesis and inhibitor studies. Thus, E(rns)E1 is processed at a novel type of signal peptidase cleavage site showing a different membrane topology. Prevention of glycosylation or introduction of mutations into the C-terminal region of E(rns) severely impairs processing, presumably by preventing proper membrane interaction or disturbing a conformation critical for the protein to be accepted as a substrate by signal peptidase.
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Affiliation(s)
- Ioana Bintintan
- Institut für Immunologie, Friedrich-Loeffler-Institut, Paul-Ehrlich-Strasse 28, D-72001 Tübingen, Germany
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Choo KH, Tan TW, Ranganathan S. A comprehensive assessment of N-terminal signal peptides prediction methods. BMC Bioinformatics 2009; 10 Suppl 15:S2. [PMID: 19958512 PMCID: PMC2788353 DOI: 10.1186/1471-2105-10-s15-s2] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Background Amino-terminal signal peptides (SPs) are short regions that guide the targeting of secretory proteins to the correct subcellular compartments in the cell. They are cleaved off upon the passenger protein reaching its destination. The explosive growth in sequencing technologies has led to the deposition of vast numbers of protein sequences necessitating rapid functional annotation techniques, with subcellular localization being a key feature. Of the myriad software prediction tools developed to automate the task of assigning the SP cleavage site of these new sequences, we review here, the performance and reliability of commonly used SP prediction tools. Results The available signal peptide data has been manually curated and organized into three datasets representing eukaryotes, Gram-positive and Gram-negative bacteria. These datasets are used to evaluate thirteen prediction tools that are publicly available. SignalP (both the HMM and ANN versions) maintains consistency and achieves the best overall accuracy in all three benchmarking experiments, ranging from 0.872 to 0.914 although other prediction tools are narrowing the performance gap. Conclusion The majority of the tools evaluated in this study encounter no difficulty in discriminating between secretory and non-secretory proteins. The challenge clearly remains with pinpointing the correct SP cleavage site. The composite scoring schemes employed by SignalP may help to explain its accuracy. Prediction task is divided into a number of separate steps, thus allowing each score to tackle a particular aspect of the prediction.
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Affiliation(s)
- Khar Heng Choo
- Institute for Infocomm Research, 1 Fusionopolis Way, #21-01 Connexis, Singapore.
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Abstract
The 2008 annual conference of the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation set up in 1998, was organized as the 7th International Conference on Bioinformatics (InCoB), jointly with the Bioinformatics and Systems Biology in Taiwan (BIT 2008) Conference, Oct. 20-23, 2008 at Taipei, Taiwan. Besides bringing together scientists from the field of bioinformatics in this region, InCoB is actively involving researchers from the area of systems biology, to facilitate greater synergy between these two groups. Marking the 10th Anniversary of APBioNet, this InCoB 2008 meeting followed on from a series of successful annual events in Bangkok (Thailand), Penang (Malaysia), Auckland (New Zealand), Busan (South Korea), New Delhi (India) and Hong Kong. Additionally, tutorials and the Workshop on Education in Bioinformatics and Computational Biology (WEBCB) immediately prior to the 20th Federation of Asian and Oceanian Biochemists and Molecular Biologists (FAOBMB) Taipei Conference provided ample opportunity for inducting mainstream biochemists and molecular biologists from the region into a greater level of awareness of the importance of bioinformatics in their craft. In this editorial, we provide a brief overview of the peer-reviewed manuscripts accepted for publication herein, grouped into thematic areas. As the regional research expertise in bioinformatics matures, the papers fall into thematic areas, illustrating the specific contributions made by APBioNet to global bioinformatics efforts.
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Affiliation(s)
- Shoba Ranganathan
- Department of Chemistry and Biomolecular Sciences and ARC Centre of Excellence in Bioinformatics, Macquarie University, Sydney NSW 2109, Australia
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597
| | - Wen-Lian Hsu
- Institute of Information Science, Academia Sinica, Nankang, Taipei, Taiwan, ROC
- Department of Computer Science, National Tsing-Hua University, Hsinchu, Taiwan, ROC
| | - Ueng-Cheng Yang
- Institute of Biomedical Informatics and Center for Systems and Synthetic Biology, National Yang-Ming University, Taiwan, ROC
| | - Tin Wee Tan
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597
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