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Pathway discovery and engineering for cleavage of a β-1 lignin-derived biaryl compound. Metab Eng 2021; 65:1-10. [PMID: 33636323 DOI: 10.1016/j.ymben.2021.02.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 01/11/2021] [Accepted: 02/09/2021] [Indexed: 11/22/2022]
Abstract
Lignin biosynthesis typically results in a polymer with several inter-monomer bond linkages, and the heterogeneity of linkages presents a challenge for depolymerization processes. While several enzyme classes have been shown to cleave common dimer linkages in lignin, the pathway of bacterial β-1 spirodienone linkage cleavage has not been elucidated. Here, we identified a pathway for cleavage of 1,2-diguaiacylpropane-1,3-diol (DGPD), a β-1 linked biaryl representative of a ring-opened spirodienone linkage, in Novosphingobium aromaticivorans DSM12444. In vitro assays using cell lysates demonstrated that RS14230 (LsdE) converts DGPD to a lignostilbene intermediate, which the carotenoid oxygenase, LsdA, then converts to vanillin. A Pseudomonas putida KT2440 strain engineered with lsdEA expression catabolizes erythro-DGPD, but not threo-DGPD. We further engineered P. putida to convert DGPD to a product, cis,cis-muconic acid. Overall, this work demonstrates the potential to identify new enzymatic reactions in N. aromaticivorans and expands the biological funnel of P. putida for microbial lignin valorization.
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102
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Tolkatchev D, Kuruba B, Smith GE, Swain KD, Smith KA, Moroz N, Williams TJ, Kostyukova AS. Structural insights into the tropomodulin assembly at the pointed ends of actin filaments. Protein Sci 2021; 30:423-437. [PMID: 33206408 PMCID: PMC7784754 DOI: 10.1002/pro.4000] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 11/09/2020] [Accepted: 11/13/2020] [Indexed: 11/11/2022]
Abstract
Tropomodulins are a family of important regulators of actin dynamics at the pointed ends of actin filaments. Four isoforms of tropomodulin, Tmod1-Tmod4, are expressed in vertebrates. Binding of tropomodulin to the pointed end is dependent on tropomyosin, an actin binding protein that itself is represented in mammals by up to 40 isoforms. The understanding of the regulatory role of the tropomodulin/tropomyosin molecular diversity has been limited due to the lack of a three-dimensional structure of the tropomodulin/tropomyosin complex. In this study, we mapped tropomyosin residues interacting with two tropomyosin-binding sites of tropomodulin and generated a three-dimensional model of the tropomodulin/tropomyosin complex for each of these sites. The models were refined by molecular dynamics simulations and validated via building a self-consistent three-dimensional model of tropomodulin assembly at the pointed end. The model of the pointed-end Tmod assembly offers new insights in how Tmod binding ensures tight control over the pointed end dynamics.
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Affiliation(s)
- Dmitri Tolkatchev
- Voiland School of Chemical Engineering and BioengineeringWashington State UniversityPullmanWashingtonUSA
| | - Balaganesh Kuruba
- Voiland School of Chemical Engineering and BioengineeringWashington State UniversityPullmanWashingtonUSA
| | - Garry E. Smith
- Voiland School of Chemical Engineering and BioengineeringWashington State UniversityPullmanWashingtonUSA
| | - Kyle D. Swain
- Voiland School of Chemical Engineering and BioengineeringWashington State UniversityPullmanWashingtonUSA
| | - Kaitlin A. Smith
- Voiland School of Chemical Engineering and BioengineeringWashington State UniversityPullmanWashingtonUSA
| | - Natalia Moroz
- Voiland School of Chemical Engineering and BioengineeringWashington State UniversityPullmanWashingtonUSA
- Department of Plant PathologyWashington State UniversityPullmanWashingtonUSA
| | - Trenton J. Williams
- Voiland School of Chemical Engineering and BioengineeringWashington State UniversityPullmanWashingtonUSA
| | - Alla S. Kostyukova
- Voiland School of Chemical Engineering and BioengineeringWashington State UniversityPullmanWashingtonUSA
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Aza P, de Salas F, Molpeceres G, Rodríguez-Escribano D, de la Fuente I, Camarero S. Protein Engineering Approaches to Enhance Fungal Laccase Production in S. cerevisiae. Int J Mol Sci 2021; 22:ijms22031157. [PMID: 33503813 PMCID: PMC7866195 DOI: 10.3390/ijms22031157] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/18/2021] [Accepted: 01/21/2021] [Indexed: 12/03/2022] Open
Abstract
Laccases secreted by saprotrophic basidiomycete fungi are versatile biocatalysts able to oxidize a wide range of aromatic compounds using oxygen as the sole requirement. Saccharomyces cerevisiae is a preferred host for engineering fungal laccases. To assist the difficult secretion of active enzymes by yeast, the native signal peptide is usually replaced by the preproleader of S. cerevisiae alfa mating factor (MFα1). However, in most cases, only basal enzyme levels are obtained. During directed evolution in S. cerevisiae of laccases fused to the α-factor preproleader, we demonstrated that mutations accumulated in the signal peptide notably raised enzyme secretion. Here we describe different protein engineering approaches carried out to enhance the laccase activity detected in the liquid extracts of S. cerevisiae cultures. We demonstrate the improved secretion of native and engineered laccases by using the fittest mutated α-factor preproleader obtained through successive laccase evolution campaigns in our lab. Special attention is also paid to the role of protein N-glycosylation in laccase production and properties, and to the introduction of conserved amino acids through consensus design enabling the expression of certain laccases otherwise not produced by the yeast. Finally, we revise the contribution of mutations accumulated in laccase coding sequence (CDS) during previous directed evolution campaigns that facilitate enzyme production.
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104
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Shey RA, Ghogomu SM, Shintouo CM, Nkemngo FN, Nebangwa DN, Esoh K, Yaah NE, Manka’aFri M, Nguve JE, Ngwese RA, Njume FN, Bertha FA, Ayong L, Njemini R, Vanhamme L, Souopgui J. Computational Design and Preliminary Serological Analysis of a Novel Multi-Epitope Vaccine Candidate against Onchocerciasis and Related Filarial Diseases. Pathogens 2021; 10:99. [PMID: 33494344 PMCID: PMC7912539 DOI: 10.3390/pathogens10020099] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 01/14/2021] [Accepted: 01/18/2021] [Indexed: 11/16/2022] Open
Abstract
: Onchocerciasis is a skin and eye disease that exerts a heavy socio-economic burden, particularly in sub-Saharan Africa, a region which harbours greater than 96% of either infected or at-risk populations. The elimination plan for the disease is currently challenged by many factors including amongst others; the potential emergence of resistance to the main chemotherapeutic agent, ivermectin (IVM). Novel tools, including preventative and therapeutic vaccines, could provide additional impetus to the disease elimination tool portfolio. Several observations in both humans and animals have provided evidence for the development of both natural and artificial acquired immunity. In this study, immuno-informatics tools were applied to design a filarial-conserved multi-epitope subunit vaccine candidate, (designated Ov-DKR-2) consisting of B-and T-lymphocyte epitopes of eight immunogenic antigens previously assessed in pre-clinical studies. The high-percentage conservation of the selected proteins and epitopes predicted in related nematode parasitic species hints that the generated chimera may be instrumental for cross-protection. Bioinformatics analyses were employed for the prediction, refinement, and validation of the 3D structure of the Ov-DKR-2 chimera. In-silico immune simulation projected significantly high levels of IgG1, T-helper, T-cytotoxic cells, INF-γ, and IL-2 responses. Preliminary immunological analyses revealed that the multi-epitope vaccine candidate reacted with antibodies in sera from both onchocerciasis-infected individuals, endemic normals as well as loiasis-infected persons but not with the control sera from European individuals. These results support the premise for further characterisation of the engineered protein as a vaccine candidate for onchocerciasis.
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Affiliation(s)
- Robert Adamu Shey
- Department of Biochemistry and Molecular Biology, Faculty of Science, University of Buea, Buea 99999, Cameroon; (R.A.S.); (S.M.G.); (C.M.S.); (D.N.N.); (N.E.Y.); (M.M.); (J.E.N.); (R.A.N.); (F.N.N.)
- Department of Molecular Biology, Institute of Biology and Molecular Medicine, IBMM, Université Libre de Bruxelles, Gosselies Campus, 6040 Gosselies, Belgium;
| | - Stephen Mbigha Ghogomu
- Department of Biochemistry and Molecular Biology, Faculty of Science, University of Buea, Buea 99999, Cameroon; (R.A.S.); (S.M.G.); (C.M.S.); (D.N.N.); (N.E.Y.); (M.M.); (J.E.N.); (R.A.N.); (F.N.N.)
| | - Cabirou Mounchili Shintouo
- Department of Biochemistry and Molecular Biology, Faculty of Science, University of Buea, Buea 99999, Cameroon; (R.A.S.); (S.M.G.); (C.M.S.); (D.N.N.); (N.E.Y.); (M.M.); (J.E.N.); (R.A.N.); (F.N.N.)
- Frailty in Ageing Research Group, Vrije Universiteit Brussel, Laarbeeklaan 103, B-1090 Brussels, Belgium;
- Department of Gerontology, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Laarbeeklaan 103, B-1090 Brussels, Belgium
| | - Francis Nongley Nkemngo
- Department of Microbiology and Parasitology, Faculty of Science, University of Buea, Buea 99999, Cameroon;
- Centre for Research in Infectious Diseases (CRID), Department of Parasitology and Medical Entomology, Yaounde BP 13591, Cameroon
| | - Derrick Neba Nebangwa
- Department of Biochemistry and Molecular Biology, Faculty of Science, University of Buea, Buea 99999, Cameroon; (R.A.S.); (S.M.G.); (C.M.S.); (D.N.N.); (N.E.Y.); (M.M.); (J.E.N.); (R.A.N.); (F.N.N.)
| | - Kevin Esoh
- Division of Human Genetics, Health Sciences Campus, Department of Pathology, University of Cape Town, Anzio Rd, Observatory, Cape Town 7925, South Africa;
| | - Ntang Emmaculate Yaah
- Department of Biochemistry and Molecular Biology, Faculty of Science, University of Buea, Buea 99999, Cameroon; (R.A.S.); (S.M.G.); (C.M.S.); (D.N.N.); (N.E.Y.); (M.M.); (J.E.N.); (R.A.N.); (F.N.N.)
| | - Muyanui Manka’aFri
- Department of Biochemistry and Molecular Biology, Faculty of Science, University of Buea, Buea 99999, Cameroon; (R.A.S.); (S.M.G.); (C.M.S.); (D.N.N.); (N.E.Y.); (M.M.); (J.E.N.); (R.A.N.); (F.N.N.)
| | - Joel Ebai Nguve
- Department of Biochemistry and Molecular Biology, Faculty of Science, University of Buea, Buea 99999, Cameroon; (R.A.S.); (S.M.G.); (C.M.S.); (D.N.N.); (N.E.Y.); (M.M.); (J.E.N.); (R.A.N.); (F.N.N.)
| | - Roland Akwelle Ngwese
- Department of Biochemistry and Molecular Biology, Faculty of Science, University of Buea, Buea 99999, Cameroon; (R.A.S.); (S.M.G.); (C.M.S.); (D.N.N.); (N.E.Y.); (M.M.); (J.E.N.); (R.A.N.); (F.N.N.)
| | - Ferdinand Ngale Njume
- Department of Biochemistry and Molecular Biology, Faculty of Science, University of Buea, Buea 99999, Cameroon; (R.A.S.); (S.M.G.); (C.M.S.); (D.N.N.); (N.E.Y.); (M.M.); (J.E.N.); (R.A.N.); (F.N.N.)
- Department of Molecular Biology, Institute of Biology and Molecular Medicine, IBMM, Université Libre de Bruxelles, Gosselies Campus, 6040 Gosselies, Belgium;
| | - Fru Asa Bertha
- Department of Public Health and Hygiene, Faculty of Health Science, University of Buea, Buea 99999, Cameroon;
| | - Lawrence Ayong
- Malaria Research Unit, Centre Pasteur Cameroon, Yaoundé Rue 2005, Cameroon;
| | - Rose Njemini
- Frailty in Ageing Research Group, Vrije Universiteit Brussel, Laarbeeklaan 103, B-1090 Brussels, Belgium;
- Department of Gerontology, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Laarbeeklaan 103, B-1090 Brussels, Belgium
| | - Luc Vanhamme
- Department of Molecular Biology, Institute of Biology and Molecular Medicine, IBMM, Université Libre de Bruxelles, Gosselies Campus, 6040 Gosselies, Belgium;
| | - Jacob Souopgui
- Department of Molecular Biology, Institute of Biology and Molecular Medicine, IBMM, Université Libre de Bruxelles, Gosselies Campus, 6040 Gosselies, Belgium;
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105
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Benedetti M, Vecchi V, Guardini Z, Dall’Osto L, Bassi R. Expression of a Hyperthermophilic Cellobiohydrolase in Transgenic Nicotiana tabacum by Protein Storage Vacuole Targeting. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1799. [PMID: 33353085 PMCID: PMC7767180 DOI: 10.3390/plants9121799] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 11/30/2020] [Accepted: 12/15/2020] [Indexed: 02/01/2023]
Abstract
Plant expression of microbial Cell Wall Degrading Enzymes (CWDEs) is a valuable strategy to produce industrial enzymes at affordable cost. Unfortunately, the constitutive expression of CWDEs may affect plant fitness to variable extents, including developmental alterations, sterility and even lethality. In order to explore novel strategies for expressing CWDEs in crops, the cellobiohydrolase CBM3GH5, from the hyperthermophilic bacterium Caldicellulosiruptor saccharolyticus, was constitutively expressed in N. tabacum by targeting the enzyme both to the apoplast and to the protein storage vacuole. The apoplast targeting failed to isolate plants expressing the recombinant enzyme despite a large number of transformants being screened. On the opposite side, the targeting of the cellobiohydrolase to the protein storage vacuole led to several transgenic lines expressing CBM3GH5, with an enzyme yield of up to 0.08 mg g DW-1 (1.67 Units g DW-1) in the mature leaf tissue. The analysis of CBM3GH5 activity revealed that the enzyme accumulated in different plant organs in a developmental-dependent manner, with the highest abundance in mature leaves and roots, followed by seeds, stems and leaf ribs. Notably, both leaves and stems from transgenic plants were characterized by an improved temperature-dependent saccharification profile.
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Affiliation(s)
- Manuel Benedetti
- Dipartimento di Medicina Clinica, Sanità Pubblica, Scienze della Vita e dell’Ambiente, Università dell’Aquila, Piazzale Salvatore Tommasi 1, 67100 L’Aquila, Italy;
| | - Valeria Vecchi
- Dipartimento di Biotecnologie, Università di Verona, Strada Le Grazie 15, 37134 Verona, Italy; (V.V.); (Z.G.); (L.D.)
| | - Zeno Guardini
- Dipartimento di Biotecnologie, Università di Verona, Strada Le Grazie 15, 37134 Verona, Italy; (V.V.); (Z.G.); (L.D.)
| | - Luca Dall’Osto
- Dipartimento di Biotecnologie, Università di Verona, Strada Le Grazie 15, 37134 Verona, Italy; (V.V.); (Z.G.); (L.D.)
| | - Roberto Bassi
- Dipartimento di Biotecnologie, Università di Verona, Strada Le Grazie 15, 37134 Verona, Italy; (V.V.); (Z.G.); (L.D.)
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106
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Huynh N, Depner N, Larson R, King-Jones K. A versatile toolkit for CRISPR-Cas13-based RNA manipulation in Drosophila. Genome Biol 2020; 21:279. [PMID: 33203452 PMCID: PMC7670108 DOI: 10.1186/s13059-020-02193-y] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 11/04/2020] [Indexed: 02/08/2023] Open
Abstract
Advances in CRISPR technology have immensely improved our ability to manipulate nucleic acids, and the recent discovery of the RNA-targeting endonuclease Cas13 adds even further functionality. Here, we show that Cas13 works efficiently in Drosophila, both ex vivo and in vivo. We test 44 different Cas13 variants to identify enzymes with the best overall performance and show that Cas13 could target endogenous Drosophila transcripts in vivo with high efficiency and specificity. We also develop Cas13 applications to edit mRNAs and target mitochondrial transcripts. Our vector collection represents a versatile tool collection to manipulate gene expression at the post-transcriptional level.
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Affiliation(s)
- Nhan Huynh
- Department of Biological Sciences, University of Alberta, G-504 Biological Sciences Bldg., Edmonton, Alberta, T6G 2E9, Canada
| | - Noah Depner
- Department of Biological Sciences, University of Alberta, G-504 Biological Sciences Bldg., Edmonton, Alberta, T6G 2E9, Canada
| | - Raegan Larson
- Department of Biological Sciences, University of Alberta, G-504 Biological Sciences Bldg., Edmonton, Alberta, T6G 2E9, Canada
| | - Kirst King-Jones
- Department of Biological Sciences, University of Alberta, G-504 Biological Sciences Bldg., Edmonton, Alberta, T6G 2E9, Canada.
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107
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Municoy M, González-Benjumea A, Carro J, Aranda C, Linde D, Renau-Mínguez C, Ullrich R, Hofrichter M, Guallar V, Gutiérrez A, Martínez AT. Fatty-Acid Oxygenation by Fungal Peroxygenases: From Computational Simulations to Preparative Regio- and Stereoselective Epoxidation. ACS Catal 2020. [DOI: 10.1021/acscatal.0c03165] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Martí Municoy
- Barcelona Supercomputing Center, Jordi Girona 29, Barcelona E-08034, Spain
| | | | - Juan Carro
- Centro de Investigaciones Biológicas Margarita Salas, CSIC, Ramiro de Maeztu 9, Madrid E-28040, Spain
| | - Carmen Aranda
- Instituto de Recursos Naturales y Agrobiología de Sevilla, CSIC, Reina Mercedes 10, Seville E-41012, Spain
| | - Dolores Linde
- Centro de Investigaciones Biológicas Margarita Salas, CSIC, Ramiro de Maeztu 9, Madrid E-28040, Spain
| | - Chantal Renau-Mínguez
- Centro de Investigaciones Biológicas Margarita Salas, CSIC, Ramiro de Maeztu 9, Madrid E-28040, Spain
| | - René Ullrich
- Technische Universität Dresden, International Institute Zittau, Markt 23, Zittau D-02763, Germany
| | - Martin Hofrichter
- Technische Universität Dresden, International Institute Zittau, Markt 23, Zittau D-02763, Germany
| | - Victor Guallar
- Barcelona Supercomputing Center, Jordi Girona 29, Barcelona E-08034, Spain
- ICREA, Passeig Lluís Companys 23, Barcelona E-08010, Spain
| | - Ana Gutiérrez
- Instituto de Recursos Naturales y Agrobiología de Sevilla, CSIC, Reina Mercedes 10, Seville E-41012, Spain
| | - Angel T. Martínez
- Centro de Investigaciones Biológicas Margarita Salas, CSIC, Ramiro de Maeztu 9, Madrid E-28040, Spain
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108
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In Silico Design of a Poly-epitope Vaccine for Urinary Tract Infection Based on Conserved Antigens by Modern Vaccinology. Int J Pept Res Ther 2020. [DOI: 10.1007/s10989-020-10137-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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109
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Dastan K, Assmar M, Amirmozafari N, Ghanaei FM, Mirpour M. Design, Expression and Purification of Strongyloides stercoralis IgG4 Immunoreactive Protein (NIE) in Escherichia coli. IRANIAN JOURNAL OF PARASITOLOGY 2020; 15:341-348. [PMID: 33082798 PMCID: PMC7548455 DOI: 10.18502/ijpa.v15i3.4198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Background Strongyloidiasis is a public health concern in northern regions of Iran, caused by Strongyloides stercoralis. Auto-infection cycle can be resulted in high parasitic load, especially in immunocompromised hosts. Because of low sensitivity of stool culture and stool-based microscopy techniques, detection of antibodies in patient's sera can be an alternative diagnostic technique for detection of the nematode. In the present study, as the first step of the development of an ELISA kit for the detection of antibodies against the nematode, IgG4 immunoreactive protein (NIE) was expressed in Escherichia coli expression system, purified and verified. Methods The NIE gene sequence was retrieved from the GenBank. This sequence was codon-optimized for the expression in E. coli BL21 (DE3). The sequence was inserted into the expression vector pET-30b (+). The recombinant vector was then transferred into competent E. coli BL21 (DE3). Transformed colonies were selected and verified by colony PCR. NIE gene expression was induced with IPTG induction. The protein production was evaluated by SDS-PAGE and verified using Western blotting. Results The codon-optimized NIE gene had required parameters for expression in E. coli. NIE protein was proved and verified by SDS-PAGE and Western blotting. Conclusion NIE recombinant protein was successfully expressed in E. coli expression system in appropriate amounts. The recombinant protein can be used for developing ELISA kit in diagnosis of S. stercoralis.
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Affiliation(s)
- Katayoun Dastan
- Department of Microbiology, Faculty of Basic Sciences, Lahijan Branch, Islamic Azad University, Lahijan, Iran
| | - Mehdi Assmar
- Department of Microbiology, Faculty of Basic Sciences, Lahijan Branch, Islamic Azad University, Lahijan, Iran.,Department of Parasitology, Pasteur Institute of Iran, Tehran, Iran
| | - Nour Amirmozafari
- Department of Microbiology, Faculty of Basic Sciences, Lahijan Branch, Islamic Azad University, Lahijan, Iran.,Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Fariborz Mansour Ghanaei
- Division of Gastroenterology, Faculty of Medicine, Gilan University of Medical Sciences, Gilan, Iran.,Gastrointestinal and Liver Disease Research Center, Razi Hospital, Rasht, Iran
| | - Mirsasan Mirpour
- Department of Microbiology, Faculty of Basic Sciences, Lahijan Branch, Islamic Azad University, Lahijan, Iran
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110
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Fu H, Liang Y, Zhong X, Pan Z, Huang L, Zhang H, Xu Y, Zhou W, Liu Z. Codon optimization with deep learning to enhance protein expression. Sci Rep 2020; 10:17617. [PMID: 33077783 PMCID: PMC7572362 DOI: 10.1038/s41598-020-74091-z] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 09/21/2020] [Indexed: 02/05/2023] Open
Abstract
Heterologous expression is the main approach for recombinant protein production ingenetic synthesis, for which codon optimization is necessary. The existing optimization methods are based on biological indexes. In this paper, we propose a novel codon optimization method based on deep learning. First, we introduce the concept of codon boxes, via which DNA sequences can be recoded into codon box sequences while ignoring the order of bases. Then, the problem of codon optimization can be converted to sequence annotation of corresponding amino acids with codon boxes. The codon optimization models for Escherichia Coli were trained by the Bidirectional Long-Short-Term Memory Conditional Random Field. Theoretically, deep learning is a good method to obtain the distribution characteristics of DNA. In addition to the comparison of the codon adaptation index, protein expression experiments for plasmodium falciparum candidate vaccine and polymerase acidic protein were implemented for comparison with the original sequences and the optimized sequences from Genewiz and ThermoFisher. The results show that our method for enhancing protein expression is efficient and competitive.
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Affiliation(s)
- Hongguang Fu
- University of Electronic Science and Technology of China, Chengdu, 611731, China
| | - Yanbing Liang
- University of Electronic Science and Technology of China, Chengdu, 611731, China
| | - Xiuqin Zhong
- University of Electronic Science and Technology of China, Chengdu, 611731, China.
| | - ZhiLing Pan
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Lei Huang
- University of Electronic Science and Technology of China, Chengdu, 611731, China
| | - HaiLin Zhang
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yang Xu
- University of Electronic Science and Technology of China, Chengdu, 611731, China
| | - Wei Zhou
- University of Electronic Science and Technology of China, Chengdu, 611731, China
| | - Zhong Liu
- Chengdu Institute of Computer Applications, Chinese Academy of Sciences, Chengdu, 610041, China
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111
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Safavi A, Kefayat A, Mahdevar E, Abiri A, Ghahremani F. Exploring the out of sight antigens of SARS-CoV-2 to design a candidate multi-epitope vaccine by utilizing immunoinformatics approaches. Vaccine 2020; 38:7612-7628. [PMID: 33082015 PMCID: PMC7546226 DOI: 10.1016/j.vaccine.2020.10.016] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 08/25/2020] [Accepted: 10/06/2020] [Indexed: 12/12/2022]
Abstract
SARS-CoV-2 causes a severe respiratory disease called COVID-19. Currently, global health is facing its devastating outbreak. However, there is no vaccine available against this virus up to now. In this study, a novel multi-epitope vaccine against SARS-CoV-2 was designed to provoke both innate and adaptive immune responses. The immunodominant regions of six non-structural proteins (nsp7, nsp8, nsp9, nsp10, nsp12 and nsp14) of SARS-CoV-2 were selected by multiple immunoinformatic tools to provoke T cell immune response. Also, immunodominant fragment of the functional region of SARS-CoV-2 spike (400-510 residues) protein was selected for inducing neutralizing antibodies production. The selected regions' sequences were connected to each other by furin-sensitive linker (RVRR). Moreover, the functional region of β-defensin as a well-known agonist for the TLR-4/MD complex was added at the N-terminus of the vaccine using (EAAAK)3 linker. Also, a CD4 + T-helper epitope, PADRE, was used at the C-terminal of the vaccine by GPGPG and A(EAAAK)2A linkers to form the final vaccine construct. The physicochemical properties, allergenicity, antigenicity, functionality and population coverage of the final vaccine construct were analyzed. The final vaccine construct was an immunogenic, non-allergen and unfunctional protein which contained multiple CD8 + and CD4 + overlapping epitopes, IFN-γ inducing epitopes, linear and conformational B cell epitopes. It could form stable and significant interactions with TLR-4/MD according to molecular docking and dynamics simulations. Global population coverage of the vaccine for HLA-I and II were estimated 96.2% and 97.1%, respectively. At last, the final vaccine construct was reverse translated to design the DNA vaccine. Although the designed vaccine exhibited high efficacy in silico, further experimental validation is necessary.
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Affiliation(s)
- Ashkan Safavi
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Amirhosein Kefayat
- Department of Oncology, Cancer Prevention Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Elham Mahdevar
- Department of Biology, Faculty of Science and Engineering, Science and Arts University, Yazd, Iran
| | - Ardavan Abiri
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran
| | - Fatemeh Ghahremani
- Department of Medical Physics and Radiotherapy, Arak School of Paramedicine, Arak University of Medical Sciences, Arak, Iran.
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Colarusso A, Lauro C, Calvanese M, Parrilli E, Tutino ML. Improvement of Pseudoalteromonas haloplanktis TAC125 as a Cell Factory: IPTG-Inducible Plasmid Construction and Strain Engineering. Microorganisms 2020; 8:microorganisms8101466. [PMID: 32987756 PMCID: PMC7598627 DOI: 10.3390/microorganisms8101466] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 09/19/2020] [Accepted: 09/22/2020] [Indexed: 02/06/2023] Open
Abstract
Our group has used the marine bacterium Pseudoalteromonas haloplanktis TAC125 (PhTAC125) as a platform for the successful recombinant production of “difficult” proteins, including eukaryotic proteins, at low temperatures. However, there is still room for improvement both in the refinement of PhTAC125 expression plasmids and in the bacterium’s intrinsic ability to accumulate and handle heterologous products. Here, we present an integrated approach of plasmid design and strain engineering finalized to increment the recombinant expression and optimize the inducer uptake in PhTAC125. To this aim, we developed the IPTG-inducible plasmid pP79 and an engineered PhTAC125 strain called KrPL LacY+. This mutant was designed to express the E. coli lactose permease and to produce only a truncated version of the endogenous Lon protease through an integration-deletion strategy. In the wild-type strain, pP79 assured a significantly better production of two reporters in comparison to the most recent expression vector employed in PhTAC125. Nevertheless, the use of KrPL LacY+ was crucial to achieving satisfying production levels using reasonable IPTG concentrations, even at 0 °C. Both the wild-type and the mutant recombinant strains are characterized by an average graded response upon IPTG induction and they will find different future applications depending on the desired levels of expression.
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113
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Calcott MJ, Owen JG, Ackerley DF. Efficient rational modification of non-ribosomal peptides by adenylation domain substitution. Nat Commun 2020; 11:4554. [PMID: 32917865 PMCID: PMC7486941 DOI: 10.1038/s41467-020-18365-0] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 08/19/2020] [Indexed: 12/22/2022] Open
Abstract
Non-ribosomal peptide synthetase (NRPS) enzymes form modular assembly-lines, wherein each module governs the incorporation of a specific monomer into a short peptide product. Modules are comprised of one or more key domains, including adenylation (A) domains, which recognise and activate the monomer substrate; condensation (C) domains, which catalyse amide bond formation; and thiolation (T) domains, which shuttle reaction intermediates between catalytic domains. This arrangement offers prospects for rational peptide modification via substitution of substrate-specifying domains. For over 20 years, it has been considered that C domains play key roles in proof-reading the substrate; a presumption that has greatly complicated rational NRPS redesign. Here we present evidence from both directed and natural evolution studies that any substrate-specifying role for C domains is likely to be the exception rather than the rule, and that novel non-ribosomal peptides can be generated by substitution of A domains alone. We identify permissive A domain recombination boundaries and show that these allow us to efficiently generate modified pyoverdine peptides at high yields. We further demonstrate the transferability of our approach in the PheATE-ProCAT model system originally used to infer C domain substrate specificity, generating modified dipeptide products at yields that are inconsistent with the prevailing dogma.
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Affiliation(s)
- Mark J Calcott
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
- Centre for Biodiscovery and Maurice Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, Wellington, New Zealand
| | - Jeremy G Owen
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
- Centre for Biodiscovery and Maurice Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, Wellington, New Zealand
| | - David F Ackerley
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand.
- Centre for Biodiscovery and Maurice Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, Wellington, New Zealand.
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114
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Nguyen AD, Kim D, Lee EY. Unlocking the biosynthesis of sesquiterpenoids from methane via the methylerythritol phosphate pathway in methanotrophic bacteria, using α-humulene as a model compound. Metab Eng 2020; 61:69-78. [PMID: 32387228 DOI: 10.1016/j.ymben.2020.04.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 03/21/2020] [Accepted: 04/25/2020] [Indexed: 11/22/2022]
Abstract
Isoprenoids are an abundant and diverse class of natural products with various applications in the pharmaceutical, cosmetics and biofuel industries. A methanotroph-based biorefinery is an attractive scenario for the production of a variety of value-added compounds from methane, because methane is a promising alternative feedstock for industrial biomanufacturing. In this study, we metabolically engineered Methylotuvimicrobium alcaliphilum 20Z for de novo synthesis of a sesquiterpenoid from methane, using α-humulene as a model compound, via optimization of the native methylerythritol phosphate (MEP) pathway. Expression of codon-optimized α-humulene synthase from Zingiber zerumbet in M. alcaliphilum 20Z resulted in an initial yield of 0.04 mg/g dry cell weight. Overexpressing key enzymes (IspA, IspG, and Dxs) for debottlenecking of the MEP pathway increased α-humulene production 5.2-fold compared with the initial strain. Subsequently, redirecting the carbon flux through the Embden-Meyerhof-Parnas pathway resulted in an additional 3-fold increase in α-humulene production. Additionally, a genome-scale model using flux scanning based on enforced objective flux method was used to identify potential overexpression targets to increase flux towards isoprenoid production. Several target reactions from cofactor synthesis pathways were probed and evaluated for their effects on α-humulene synthesis, resulting in α-humulene yield up to 0.75 mg/g DCW with 18.8-fold enhancement from initial yield. This study first demonstrates production of a sesquiterpenoid from methane using methanotrophs as the biocatalyst and proposes potential strategies to enhance production of sesquiterpenoid and related isoprenoid products in engineered methanotrophic bacteria.
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Affiliation(s)
- Anh Duc Nguyen
- Department of Chemical Engineering, Kyung Hee University, Yongin-si, Gyeonggi-do, 17104, South Korea
| | - Donghyuk Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, South Korea
| | - Eun Yeol Lee
- Department of Chemical Engineering, Kyung Hee University, Yongin-si, Gyeonggi-do, 17104, South Korea.
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115
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Designing an HCV diagnostic kit for common genotypes of the virus in Iran based on conserved regions of core, NS3-protease, NS4A/B, and NS5A/B antigens: an in silico approach. Biologia (Bratisl) 2020. [DOI: 10.2478/s11756-020-00566-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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116
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Wang SE, Brooks AES, Poole AM, Simoes-Barbosa A. Determinants of translation efficiency in the evolutionarily-divergent protist Trichomonas vaginalis. BMC Mol Cell Biol 2020; 21:54. [PMID: 32689943 PMCID: PMC7370421 DOI: 10.1186/s12860-020-00297-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 06/29/2020] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Trichomonas vaginalis, the causative agent of a prevalent urogenital infection in humans, is an evolutionarily divergent protozoan. Protein-coding genes in T. vaginalis are largely controlled by two core promoter elements, producing mRNAs with short 5' UTRs. The specific mechanisms adopted by T. vaginalis to fine-tune the translation efficiency (TE) of mRNAs remain largely unknown. RESULTS Using both computational and experimental approaches, this study investigated two key factors influencing TE in T. vaginalis: codon usage and mRNA secondary structure. Statistical dependence between TE and codon adaptation index (CAI) highlighted the impact of codon usage on mRNA translation in T. vaginalis. A genome-wide interrogation revealed that low structural complexity at the 5' end of mRNA followed closely by a highly structured downstream region correlates with TE variation in this organism. To validate these findings, a synthetic library of 15 synonymous iLOV genes was created, representing five mRNA folding profiles and three codon usage profiles. Fluorescence signals produced by the expression of these synonymous iLOV genes in T. vaginalis were consistent with and validated our in silico predictions. CONCLUSIONS This study demonstrates the role of codon usage bias and mRNA secondary structure in TE of T. vaginalis mRNAs, contributing to a better understanding of the factors that influence, and possibly regulate, gene expression in this human pathogen.
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Affiliation(s)
- Shuqi E Wang
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, USA
| | - Anna E S Brooks
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
- Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand
| | - Anthony M Poole
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
- Bioinformatics Institute, The University of Auckland, Auckland, New Zealand
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117
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Klug D, Goellner S, Kehrer J, Sattler J, Strauss L, Singer M, Lu C, Springer TA, Frischknecht F. Evolutionarily distant I domains can functionally replace the essential ligand-binding domain of Plasmodium TRAP. eLife 2020; 9:57572. [PMID: 32648541 PMCID: PMC7351488 DOI: 10.7554/elife.57572] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 06/25/2020] [Indexed: 02/02/2023] Open
Abstract
Inserted (I) domains function as ligand-binding domains in adhesins that support cell adhesion and migration in many eukaryotic phyla. These adhesins include integrin αβ heterodimers in metazoans and single subunit transmembrane proteins in apicomplexans such as TRAP in Plasmodium and MIC2 in Toxoplasma. Here we show that the I domain of TRAP is essential for sporozoite gliding motility, mosquito salivary gland invasion and mouse infection. Its replacement with the I domain from Toxoplasma MIC2 fully restores tissue invasion and parasite transmission, while replacement with the aX I domain from human integrins still partially restores liver infection. Mutations around the ligand binding site allowed salivary gland invasion but led to inefficient transmission to the rodent host. These results suggest that apicomplexan parasites appropriated polyspecific I domains in part for their ability to engage with multiple ligands and to provide traction for emigration into diverse organs in distant phyla. Malaria is an infectious disease caused by single-celled parasites known as Plasmodium. Humans and other animals with backbones – such as birds, reptiles and rodents – can become hosts for these parasites if an infected female mosquito feeds on their blood. Likewise, healthy mosquitoes can in turn become infected with Plasmodium if they feed on the blood of an infected animal. To complete their life cycle, Plasmodium parasites within a mosquito must become spore-like cells called sporozoites. These sporozoites are highly mobile and can get into the mosquitoes’ salivary glands, meaning they can be passed on to a new host when the insect feeds. During a mosquito bite the sporozoites are spat into the skin of the potential host, where they then need to migrate rapidly to enter the bloodstream. Once in the blood, the sporozoites can then get into liver cells and begin a new infection. One protein called TRAP, which is found on the surface of the sporozoites, is important for their migration and the infection of the salivary glands or liver. Yet it was not known how this happens at the level of the individual proteins involved. Klug et al. have now tested how a part of the TRAP protein, called the I domain, contributes to the infection process. In the experiments, the I domain of TRAP was deleted which showed that the sporozoites need this domain to be able to move around and get into the host tissues. Without the I domain the sporozoites were stuck and could not successfully infect either the mosquitoes, the livers of mice, or human liver cells grown in the laboratory. Klug et al. then replaced the Plasmodium I domain of TRAP with the I domain from a distantly related parasite called Toxoplasma gondii, which causes a condition known as toxoplasmosis. The I domain from Toxoplasma allowed the Plasmodium parasites to infect the host tissues again. This observation was unexpected because Toxoplasma and Plasmodium parasites have evolved separately over the last 800 million years and Toxoplasma does not infect insects. These findings suggest that the I domain of TRAP evolved to bind several other proteins in different tissues and hosts. Future studies will investigate which other parasite proteins TRAP works with to guide sporozoites to the salivary glands or liver. Knowledge of how these proteins act together may lead to new approaches for treating or preventing malaria. For example, some treatments could stop sporozoites from entering liver cells.
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Affiliation(s)
- Dennis Klug
- Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Medical School, Heidelberg, Germany.,Université de Strasbourg, CNRS UPR9022, INSERM U963, Institut de Biologie Moléculaire et Cellulaire, Strasbourg, France
| | - Sarah Goellner
- Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Medical School, Heidelberg, Germany.,Department of Molecular Virology, Heidelberg University Medical School, Heidelberg, Germany
| | - Jessica Kehrer
- Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Medical School, Heidelberg, Germany
| | - Julia Sattler
- Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Medical School, Heidelberg, Germany
| | - Léanne Strauss
- Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Medical School, Heidelberg, Germany
| | - Mirko Singer
- Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Medical School, Heidelberg, Germany.,Experimental Parasitology, Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität München, München, Germany
| | - Chafen Lu
- Program in Cellular and Molecular Medicine, Children's Hospital Boston, and Departments of Biological Chemistry and Molecular Pharmacology and of Medicine, Harvard Medical School, Boston, United States
| | - Timothy A Springer
- Program in Cellular and Molecular Medicine, Children's Hospital Boston, and Departments of Biological Chemistry and Molecular Pharmacology and of Medicine, Harvard Medical School, Boston, United States
| | - Friedrich Frischknecht
- Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Medical School, Heidelberg, Germany
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118
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Gonçalves CDC, Pinheiro GMS, Dahlström KM, Souto DEP, Kubota LT, Barbosa LRS, Ramos CHI. On the structure and function of Sorghum bicolor CHIP (carboxyl terminus of Hsc70-interacting protein): A link between chaperone and proteasome systems. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 296:110506. [PMID: 32540021 DOI: 10.1016/j.plantsci.2020.110506] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 04/12/2020] [Accepted: 04/18/2020] [Indexed: 06/11/2023]
Abstract
The co-chaperone CHIP (carboxy terminus of Hsc70 interacting protein) is very important for many cell activities since it regulates the ubiquitination of substrates targeted for proteasomal degradation. However, information on the structure-function relationship of CHIP from plants and how it interacts and ubiquitinates other plant chaperones is still needed. For that, the CHIP ortholog from Sorghum bicolor (SbCHIP) was identified and studied in detail. SbCHIP was purified and produced folded and pure, being capable of keeping its structural conformation up to 42 °C, indicating that cellular function is maintained even in a hot environment. Also, SbCHIP was able to bind plant Hsp70 and Hsp90 with high affinity and interact with E2 enzymes, performing E3 ligase activity. The data allowed to reveal the pattern of plant Hsp70 and Hsp90 ubiquitination and described which plant E2 enzymes are likely involved in SbCHIP-mediated ubiquitination. Aditionally, we obtained information on the SbCHIP conformation, showing that it is a non-globular symmetric dimer and allowing to put forward a model for the interaction of SbCHIP with chaperones and E2 enzymes that suggests a mechanism of ubiquitination. Altogether, the results presented here are useful additions to the study of protein folding and degradation in plants.
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Affiliation(s)
| | - Glaucia M S Pinheiro
- Institute of Chemistry, University of Campinas-UNICAMP, Campinas, SP 13083-970, Brazil
| | - Käthe M Dahlström
- Institute of Chemistry, University of Campinas-UNICAMP, Campinas, SP 13083-970, Brazil
| | - Dênio E P Souto
- Institute of Chemistry, University of Campinas-UNICAMP, Campinas, SP 13083-970, Brazil
| | - Lauro T Kubota
- Institute of Chemistry, University of Campinas-UNICAMP, Campinas, SP 13083-970, Brazil
| | - Leandro R S Barbosa
- Institute of Physics, University of São Paulo-USP, São Paulo, SP 05508-090, Brazil
| | - Carlos H I Ramos
- Institute of Chemistry, University of Campinas-UNICAMP, Campinas, SP 13083-970, Brazil.
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119
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Digiovanni S, Visentin C, Degani G, Barbiroli A, Chiara M, Regazzoni L, Di Pisa F, Borchert AJ, Downs DM, Ricagno S, Vanoni MA, Popolo L. Two novel fish paralogs provide insights into the Rid family of imine deaminases active in pre-empting enamine/imine metabolic damage. Sci Rep 2020; 10:10135. [PMID: 32576850 PMCID: PMC7311433 DOI: 10.1038/s41598-020-66663-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 05/12/2020] [Indexed: 12/17/2022] Open
Abstract
Reactive Intermediate Deaminase (Rid) protein superfamily includes eight families among which the RidA is conserved in all domains of life. RidA proteins accelerate the deamination of the reactive 2-aminoacrylate (2AA), an enamine produced by some pyridoxal phosphate (PLP)-dependent enzymes. 2AA accumulation inhibits target enzymes with a detrimental impact on fitness. As a consequence of whole genome duplication, teleost fish have two ridA paralogs, while other extant vertebrates contain a single-copy gene. We investigated the biochemical properties of the products of two paralogs, identified in Salmo salar. SsRidA-1 and SsRidA-2 complemented the growth defect of a Salmonella enterica ridA mutant, an in vivo model of 2AA stress. In vitro, both proteins hydrolyzed 2-imino acids (IA) to keto-acids and ammonia. SsRidA-1 was active on IA derived from nonpolar amino acids and poorly active or inactive on IA derived from other amino acids tested. In contrast, SsRidA-2 had a generally low catalytic efficiency, but showed a relatively higher activity with IA derived from L-Glu and aromatic amino acids. The crystal structures of SsRidA-1 and SsRidA-2 provided hints of the remarkably different conformational stability and substrate specificity. Overall, SsRidA-1 is similar to the mammalian orthologs whereas SsRidA-2 displays unique properties likely generated by functional specialization of a duplicated ancestral gene.
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Affiliation(s)
- Stefania Digiovanni
- Department of Biosciences, University of Milan, Milan, Italy.,Department of Chemical Biology I, University of Groningen, Groningen, The Netherlands
| | | | - Genny Degani
- Department of Biosciences, University of Milan, Milan, Italy
| | - Alberto Barbiroli
- Department of Food, Environmental and Nutritional Sciences, University of Milan, Milan, Italy
| | - Matteo Chiara
- Department of Biosciences, University of Milan, Milan, Italy
| | - Luca Regazzoni
- Department of Pharmaceutical Sciences, University of Milan, Milan, Italy
| | - Flavio Di Pisa
- Department of Biosciences, University of Milan, Milan, Italy
| | - Andrew J Borchert
- Department of Microbiology, University of Georgia, Athens, GA, United States.,National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Diana M Downs
- Department of Microbiology, University of Georgia, Athens, GA, United States
| | - Stefano Ricagno
- Department of Biosciences, University of Milan, Milan, Italy
| | | | - Laura Popolo
- Department of Biosciences, University of Milan, Milan, Italy.
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120
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Mycobacterium lepromatosis genome exhibits unusually high CpG dinucleotide content and selection is key force in shaping codon usage. INFECTION GENETICS AND EVOLUTION 2020; 84:104399. [PMID: 32512206 DOI: 10.1016/j.meegid.2020.104399] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 05/30/2020] [Accepted: 06/03/2020] [Indexed: 01/06/2023]
Abstract
Mycobacterium lepromatosis was identified as a causative agent for leprosy in the year 2008 in the United States and later more cases were identified in Canada, Singapore, Brazil, and Myanmar. It is known to cause diffuse lepromatosis leprosy among humans. Since it is invasive, the mortality rates are higher in comparison to the M. leprae. At genomic level, there exists 90.9% similarity between M. lepromatosis and M. leprae. Codon usage analysis based on analyses of 228 coding sequences (CDSs) of M. lepromatosis, revealed that the genome is GC rich. Among the total 16 dinucleotides, CpG dinucleotide possesses the highest dinucleotide frequency in M. lepromatosis, that is strikingly an unobvious observation since higher CpG is associated with higher proinflammatory cytokine production and NF-κB activation that eventually leads to high pathogenicity. To evade immune response, CpG content is generally less in pathogens. The unusually high CpG content can be explained by the fact that the nucleotide composition of M. lepromatosis is CG rich. Various forces interplay to shape codon usage pattern of any organism including selection; mutation, nucleotide composition as well as GC biased gene conversion. To understand the interplay between various forces; neutrality, parity, Nc-GC3 (Effective number of codons-GC content at 3rd position of the codon), aromaticity (AROMO) and the general average hydropathicity score (GRAVY) analyses have been carried out. The analyses revealed that selection force is the major contributory force. Along with the selection; mutation, nucleotide composition as well as GC biased gene conversion also play role in shaping codon usage bias in M. lepromatosis. This is the first report on the codon usage in M. lepromatosis.
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121
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Saez-Jimenez V, Maršić ŽS, Lambrughi M, Shin JH, van Havere R, Papaleo E, Olsson L, Mapelli V. Structure-function investigation of 3-methylaspartate ammonia lyase reveals substrate molecular determinants for the deamination reaction. PLoS One 2020; 15:e0233467. [PMID: 32437404 PMCID: PMC7241714 DOI: 10.1371/journal.pone.0233467] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 05/05/2020] [Indexed: 12/03/2022] Open
Abstract
The enzymatic reactions leading to the deamination of β-lysine, lysine, or 2-aminoadipic acid are of great interest for the metabolic conversion of lysine to adipic acid. Enzymes able to carry out these reactions are not known, however ammonia lyases (EC 4.3.1.-) perform deamination on a wide range of substrates. We have studied 3-methylaspartate ammonia lyase (MAL, EC 4.3.1.2) as a potential candidate for protein engineering to enable deamination towards β-lysine, that we have shown to be a competitive inhibitor of MAL. We have characterized MAL activity, binding and inhibition properties on six different compounds that would allow to define the molecular determinants necessary for MAL to deaminate our substrate of interest. Docking calculations showed that β-lysine as well as the other compounds investigated could fit spatially into MAL catalytic pocket, although they probably are weak or very transient binders and we identified molecular determinants involved in the binding of the substrate. The hydrophobic interactions formed by the methyl group of 3-methylaspartic acid, together with the presence of the amino group on carbon 2, play an essential role in the appropriate binding of the substrate. The results showed that β-lysine is able to fit and bind in MAL catalytic pocket and can be potentially converted from inhibitor to substrate of MAL upon enzyme engineering. The characterization of the binding and inhibition properties of the substrates tested here provide the foundation for future and more extensive studies on engineering MAL that could lead to a MAL variant able to catalyse this challenging deamination reaction.
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Affiliation(s)
- Veronica Saez-Jimenez
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Željka Sanader Maršić
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Matteo Lambrughi
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Jae Ho Shin
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Robin van Havere
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Elena Papaleo
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Lisbeth Olsson
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Valeria Mapelli
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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122
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Wu X, Zhou H, Li L, Wang E, Zhou X, Gu Y, Wu X, Shen L, Zeng W. Whole Genome Sequencing and Comparative Genomic Analyses of Lysinibacillus pakistanensis LZH-9, a Halotolerant Strain with Excellent COD Removal Capability. Microorganisms 2020; 8:microorganisms8050716. [PMID: 32408484 PMCID: PMC7284689 DOI: 10.3390/microorganisms8050716] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/07/2020] [Accepted: 05/08/2020] [Indexed: 11/26/2022] Open
Abstract
Halotolerant microorganisms are promising in bio-treatment of hypersaline industrial wastewater. Four halotolerant bacteria strains were isolated from wastewater treatment plant, of which a strain LZH-9 could grow in the presence of up to 14% (w/v) NaCl, and it removed 81.9% chemical oxygen demand (COD) at 96 h after optimization. Whole genome sequencing of Lysinibacillus pakistanensis LZH-9 and comparative genomic analysis revealed metabolic versatility of different species of Lysinibacillus, and abundant genes involved in xenobiotics biodegradation, resistance to toxic compound, and salinity were found in all tested species of Lysinibacillus, in which Horizontal Gene Transfer (HGT) contributed to the acquisition of many important properties of Lysinibacillus spp. such as toxic compound resistance and osmotic stress resistance as revealed by phylogenetic analyses. Besides, genome wide positive selection analyses revealed seven genes that contained adaptive mutations in Lysinibacillus spp., most of which were multifunctional. Further expression assessment with Codon Adaption Index (CAI) also reflected the high metabolic rate of L. pakistanensis to digest potential carbon or nitrogen sources in organic contaminants, which was closely linked with efficient COD removal ability of strain LZH-9. The high COD removal efficiency and halotolerance as well as genomic evidences suggested that L. pakistanensis LZH-9 was promising in treating hypersaline industrial wastewater.
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Affiliation(s)
- Xueling Wu
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; (X.W.); (H.Z.); (L.L.); (E.W.); (X.Z.); (Y.G.); (X.W.); (L.S.)
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha 410083, China
| | - Han Zhou
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; (X.W.); (H.Z.); (L.L.); (E.W.); (X.Z.); (Y.G.); (X.W.); (L.S.)
| | - Liangzhi Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; (X.W.); (H.Z.); (L.L.); (E.W.); (X.Z.); (Y.G.); (X.W.); (L.S.)
| | - Enhui Wang
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; (X.W.); (H.Z.); (L.L.); (E.W.); (X.Z.); (Y.G.); (X.W.); (L.S.)
| | - Xiangyu Zhou
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; (X.W.); (H.Z.); (L.L.); (E.W.); (X.Z.); (Y.G.); (X.W.); (L.S.)
| | - Yichao Gu
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; (X.W.); (H.Z.); (L.L.); (E.W.); (X.Z.); (Y.G.); (X.W.); (L.S.)
| | - Xiaoyan Wu
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; (X.W.); (H.Z.); (L.L.); (E.W.); (X.Z.); (Y.G.); (X.W.); (L.S.)
| | - Li Shen
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; (X.W.); (H.Z.); (L.L.); (E.W.); (X.Z.); (Y.G.); (X.W.); (L.S.)
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha 410083, China
| | - Weimin Zeng
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; (X.W.); (H.Z.); (L.L.); (E.W.); (X.Z.); (Y.G.); (X.W.); (L.S.)
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha 410083, China
- Correspondence: ; Tel.: +86-0731-88877472
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Pines G, Fankhauser RG, Eckert CA. Predicting Drug Resistance Using Deep Mutational Scanning. Molecules 2020; 25:E2265. [PMID: 32403408 PMCID: PMC7248951 DOI: 10.3390/molecules25092265] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 05/05/2020] [Accepted: 05/05/2020] [Indexed: 12/12/2022] Open
Abstract
Drug resistance is a major healthcare challenge, resulting in a continuous need to develop new inhibitors. The development of these inhibitors requires an understanding of the mechanisms of resistance for a critical mass of occurrences. Recent genome editing technologies based on high-throughput DNA synthesis and sequencing may help to predict mutations resulting in resistance by testing large mutagenesis libraries. Here we describe the rationale of this approach, with examples and relevance to drug development and resistance in malaria.
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Affiliation(s)
- Gur Pines
- Department of Entomology, Agricultural Research Organization, Volcani Center, P.O.B 15159, Rishon LeZion 7505101, Israel
| | - Reilly G. Fankhauser
- Department of Dermatology, Oregon Health & Science University, Baird Hall 3225 SW Pavilion Loop, Portland, OR 97239, USA;
| | - Carrie A. Eckert
- Renewable and Sustainable Energy Institute, University of Colorado Boulder, 027 UCB, Boulder, CO 80309, USA
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA
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124
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Kim SY, Kim KW, Kwon YM, Kim JYH. mCherry Protein as an In Vivo Quantitative Reporter of Gene Expression in the Chloroplast of Chlamydomonas reinhardtii. Mol Biotechnol 2020; 62:297-305. [PMID: 32185599 DOI: 10.1007/s12033-020-00249-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Microalgal chloroplasts have a substantial potential as a sustainable alternative to conventional hosts for recombinant protein production, due to their photosynthetic ability. However, realization of microalgal chloroplast as a platform for the production of recombinant proteins has suffered from difficulties in genetic manipulation and development of molecular tools, including reporter proteins. Here, we investigated the suitability of a fluorescent protein, mCherry, as a reporter for quantitative in vivo monitoring of gene expression in the chloroplast of Chlamydomonas reinhardtii. By analyzing cell growth, the fluorescence intensity of a mCherry-expressing strain, as well as auto-fluorescence, under different photoautotrophic culture conditions, we demonstrated a strong correlation between the fluorescence intensity of mCherry expressed in the chloroplast and its protein expression level. In addition, we found that the supply of CO2 and light energy can be an important factor for the synthesis of recombinant proteins in the microalgal chloroplast. Our results identified mCherry as a reliable and quantitative reporter for the study of gene expression in chloroplasts, which is essential for the biotechnological application of microalgal chloroplasts and for improved production of valuable recombinant proteins.
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Affiliation(s)
- Sun Young Kim
- Department of Applied Research, National Marine Biodiversity Institute of Korea, Jangsan-ro 101-75, Seocheon-gun, Chungcheongnam-do, 33662, South Korea
| | - Kyung Woo Kim
- Department of Applied Research, National Marine Biodiversity Institute of Korea, Jangsan-ro 101-75, Seocheon-gun, Chungcheongnam-do, 33662, South Korea
| | - Yong Min Kwon
- Department of Applied Research, National Marine Biodiversity Institute of Korea, Jangsan-ro 101-75, Seocheon-gun, Chungcheongnam-do, 33662, South Korea
| | - Jaoon Young Hwan Kim
- Department of Applied Research, National Marine Biodiversity Institute of Korea, Jangsan-ro 101-75, Seocheon-gun, Chungcheongnam-do, 33662, South Korea.
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125
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Şen A, Kargar K, Akgün E, Pınar MÇ. Codon optimization: a mathematical programing approach. Bioinformatics 2020; 36:4012-4020. [DOI: 10.1093/bioinformatics/btaa248] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 11/25/2019] [Accepted: 04/13/2020] [Indexed: 12/11/2022] Open
Abstract
AbstractMotivationSynthesizing proteins in heterologous hosts is an important tool in biotechnology. However, the genetic code is degenerate and the codon usage is biased in many organisms. Synonymous codon changes that are customized for each host organism may have a significant effect on the level of protein expression. This effect can be measured by using metrics, such as codon adaptation index, codon pair bias, relative codon bias and relative codon pair bias. Codon optimization is designing codons that improve one or more of these objectives. Currently available algorithms and software solutions either rely on heuristics without providing optimality guarantees or are very rigid in modeling different objective functions and restrictions.ResultsWe develop an effective mixed integer linear programing (MILP) formulation, which considers multiple objectives. Our numerical study shows that this formulation can be effectively used to generate (Pareto) optimal codon designs even for very long amino acid sequences using a standard commercial solver. We also show that one can obtain designs in the efficient frontier in reasonable solution times and incorporate other complex objectives, such as mRNA secondary structures in codon design using MILP formulations.Availability and implementationhttp://alpersen.bilkent.edu.tr/codonoptimization/CodonOptimization.zip.
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Affiliation(s)
- Alper Şen
- Department of Industrial Engineering, Bilkent University, Ankara 06800, Turkey
| | - Kamyar Kargar
- Department of Industrial Engineering, Bilkent University, Ankara 06800, Turkey
| | - Esma Akgün
- Department of Management Sciences, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Mustafa Ç Pınar
- Department of Industrial Engineering, Bilkent University, Ankara 06800, Turkey
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Presenting a codon-optimized palette of fluorescent proteins for use in Candida albicans. Sci Rep 2020; 10:6158. [PMID: 32273559 PMCID: PMC7145796 DOI: 10.1038/s41598-020-63308-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 03/27/2020] [Indexed: 11/20/2022] Open
Abstract
Fluorescent proteins with varying colors are indispensable tools for the life sciences research community. These fluorophores are often developed for use in mammalian systems, with incremental enhancements or new versions published frequently. However, the successful application of these labels in other organisms in the tree of life, such as the fungus Candida albicans, can be difficult to achieve due to the difficulty in engineering constructs for good expression in these organisms. In this contribution, we present a palette of Candida-optimized fluorescent proteins ranging from cyan to red and assess their application potential. We also compare a range of reported expression optimization techniques, and find that none of these strategies is generally applicable, and that even very closely related proteins require the application of different strategies to achieve good expression. In addition to reporting new fluorescent protein variants for applications in Candida albicans, our work highlights the ongoing challenges in optimizing protein expression in heterologous systems.
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127
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Cutolo E, Tosoni M, Barera S, Herrera-Estrella L, Dall’Osto L, Bassi R. A Phosphite Dehydrogenase Variant with Promiscuous Access to Nicotinamide Cofactor Pools Sustains Fast Phosphite-Dependent Growth of Transplastomic Chlamydomonas reinhardtii. PLANTS 2020; 9:plants9040473. [PMID: 32276527 PMCID: PMC7238262 DOI: 10.3390/plants9040473] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 03/28/2020] [Accepted: 03/31/2020] [Indexed: 01/23/2023]
Abstract
Heterologous expression of the NAD+-dependent phosphite dehydrogenase (PTXD) bacterial enzyme from Pseudomonas stutzerii enables selective growth of transgenic organisms by using phosphite as sole phosphorous source. Combining phosphite fertilization with nuclear expression of the ptxD transgene was shown to be an alternative to herbicides in controlling weeds and contamination of algal cultures. Chloroplast expression of ptxD in Chlamydomonas reinhardtii was proposed as an environmentally friendly alternative to antibiotic resistance genes for plastid transformation. However, PTXD activity in the chloroplast is low, possibly due to the low NAD+/NADP+ ratio, limiting the efficiency of phosphite assimilation. We addressed the intrinsic constraints of the PTXD activity in the chloroplast and improved its catalytic efficiency in vivo via rational mutagenesis of key residues involved in cofactor binding. Transplastomic lines carrying a mutagenized PTXD version promiscuously used NADP+ and NAD+ for converting phosphite into phosphate and grew faster compared to those expressing the wild type protein. The modified PTXD enzyme also enabled faster and reproducible selection of transplastomic colonies by directly plating on phosphite-containing medium. These results allow using phosphite as selective agent for chloroplast transformation and for controlling biological contaminants when expressing heterologous proteins in algal chloroplasts, without compromising on culture performance.
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Affiliation(s)
- Edoardo Cutolo
- Laboratory of Photosynthesis and Bioenergy, Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy; (E.C.); (M.T.); (S.B.); (L.D.)
| | - Matteo Tosoni
- Laboratory of Photosynthesis and Bioenergy, Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy; (E.C.); (M.T.); (S.B.); (L.D.)
| | - Simone Barera
- Laboratory of Photosynthesis and Bioenergy, Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy; (E.C.); (M.T.); (S.B.); (L.D.)
| | - Luis Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad (UGA) Cinvestav, 36821 Irapuato, Guanajuato, Mexico;
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Sciences, Texas Tech University, Box 42122, Lubbock, TX 79409, USA
| | - Luca Dall’Osto
- Laboratory of Photosynthesis and Bioenergy, Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy; (E.C.); (M.T.); (S.B.); (L.D.)
| | - Roberto Bassi
- Laboratory of Photosynthesis and Bioenergy, Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy; (E.C.); (M.T.); (S.B.); (L.D.)
- Correspondence: ; Tel.: +39-045-802-7916
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Lambrughi M, Sanader Maršić Ž, Saez-Jimenez V, Mapelli V, Olsson L, Papaleo E. Conformational gating in ammonia lyases. Biochim Biophys Acta Gen Subj 2020; 1864:129605. [PMID: 32222547 DOI: 10.1016/j.bbagen.2020.129605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 03/11/2020] [Accepted: 03/23/2020] [Indexed: 11/17/2022]
Abstract
BACKGROUND Ammonia lyases are enzymes of industrial and biomedical interest. Knowledge of structure-dynamics-function relationship in ammonia lyases is instrumental for exploiting the potential of these enzymes in industrial or biomedical applications. METHODS We investigated the conformational changes in the proximity of the catalytic pocket of a 3-methylaspartate ammonia lyase (MAL) as a model system. At this scope, we used microsecond all-atom molecular dynamics simulations, analyzed with dimensionality reduction techniques, as well as in terms of contact networks and correlated motions. RESULTS We identify two regulatory elements in the MAL structure, i.e., the β5-α2 loop and the helix-hairpin-loop subdomain. These regulatory elements undergo conformational changes switching from 'occluded' to 'open' states. The rearrangements are coupled to changes in the accessibility of the active site. The β5-α2 loop and the helix-hairpin-loop subdomain modulate the formation of tunnels from the protein surface to the catalytic site, making the active site more accessible to the substrate when they are in an open state. CONCLUSIONS Our work pinpoints a sequential mechanism, in which the helix-hairpin-loop subdomain of MAL needs to break a subset of intramolecular interactions first to favor the displacement of the β5-α2 loop. The coupled conformational changes of these two elements contribute to modulate the accessibility of the catalytic site. GENERAL SIGNIFICANCE Similar molecular mechanisms can have broad relevance in other ammonia lyases with similar regulatory loops. Our results also imply that it is important to account for protein dynamics in the design of variants of ammonia lyases for industrial and biomedical applications.
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Affiliation(s)
- Matteo Lambrughi
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Željka Sanader Maršić
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Veronica Saez-Jimenez
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
| | - Valeria Mapelli
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
| | - Lisbeth Olsson
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
| | - Elena Papaleo
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark; Translational Disease Systems Biology, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research University of Copenhagen, Copenhagen, Denmark.
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129
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Two New Unspecific Peroxygenases from Heterologous Expression of Fungal Genes in Escherichia coli. Appl Environ Microbiol 2020; 86:AEM.02899-19. [PMID: 31980430 PMCID: PMC7082571 DOI: 10.1128/aem.02899-19] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 01/17/2020] [Indexed: 12/22/2022] Open
Abstract
UPOs catalyze regio- and stereoselective oxygenations of both aromatic and aliphatic compounds. Similar reactions were previously described for cytochrome P450 monooxygenases, but UPOs have the noteworthy biotechnological advantage of being stable enzymes requiring only H2O2 to be activated. Both characteristics are related to the extracellular nature of UPOs as secreted proteins. In the present study, the limited repertoire of UPO enzymes available for organic synthesis and other applications is expanded with the description of two new ascomycete UPOs obtained by Escherichia coli expression of the corresponding genes as soluble and active enzymes. Moreover, directed mutagenesis in E. coli, together with enzyme molecular modeling, provided relevant structure-function information on aromatic substrate oxidation by these two new biocatalysts. Unspecific peroxygenases (UPOs) constitute a new family of fungal heme-thiolate enzymes in which there is high biotechnological interest. Although several thousand genes encoding hypothetical UPO-type proteins have been identified in sequenced fungal genomes and other databases, only a few UPO enzymes have been experimentally characterized to date. Therefore, gene screening and heterologous expression from genetic databases are a priority in the search for ad hoc UPOs for oxyfunctionalization reactions of interest. Very recently, Escherichia coli production of a previously described basidiomycete UPO (as a soluble and active enzyme) has been reported. Here, we explored this convenient heterologous expression system to obtain the protein products from available putative UPO genes. In this way, two UPOs from the ascomycetes Collariella virescens (syn., Chaetomium virescens) and Daldinia caldariorum were successfully obtained, purified, and characterized. Comparison of their kinetic constants for oxidation of model substrates revealed 10- to 20-fold-higher catalytic efficiency of the latter enzyme in oxidizing simple aromatic compounds (such as veratryl alcohol, naphthalene, and benzyl alcohol). Homology molecular models of these enzymes showed three conserved and two differing residues in the distal side of the heme (the latter representing two different positions of a phenylalanine residue). Interestingly, replacement of the C. virescens UPO Phe88 by the homologous residue in the D. caldariorum UPO resulted in an F88L variant with 5- to 21-fold-higher efficiency in oxidizing these aromatic compounds. IMPORTANCE UPOs catalyze regio- and stereoselective oxygenations of both aromatic and aliphatic compounds. Similar reactions were previously described for cytochrome P450 monooxygenases, but UPOs have the noteworthy biotechnological advantage of being stable enzymes requiring only H2O2 to be activated. Both characteristics are related to the extracellular nature of UPOs as secreted proteins. In the present study, the limited repertoire of UPO enzymes available for organic synthesis and other applications is expanded with the description of two new ascomycete UPOs obtained by Escherichia coli expression of the corresponding genes as soluble and active enzymes. Moreover, directed mutagenesis in E. coli, together with enzyme molecular modeling, provided relevant structure-function information on aromatic substrate oxidation by these two new biocatalysts.
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130
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Satyam R, Bhardwaj T, Jha NK, Jha SK, Nand P. Toward a chimeric vaccine against multiple isolates of Mycobacteroides - An integrative approach. Life Sci 2020; 250:117541. [PMID: 32169520 DOI: 10.1016/j.lfs.2020.117541] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 03/07/2020] [Accepted: 03/08/2020] [Indexed: 01/31/2023]
Abstract
AIM Nontuberculous mycobacterial (NTM) infection such as endophthalmitis, dacryocystitis, and canaliculitis are pervasive across the globe and are currently managed by antibiotics. However, the recent cases of Mycobacteroides developing drug resistance reported along with the improper practice of medicine intrigued us to explore its genomic and proteomic canvas at a global scale and develop a chimeric vaccine against Mycobacteroides. MAIN METHODS We carried out a vivid genomic study on five recently sequenced strains of Mycobacteroides and explored their Pan-core genome/proteome in three different phases. The promiscuous antigenic proteins were identified via a subtractive proteomics approach that qualified for virulence causation, resistance and essentiality factors for this notorious bacterium. An integrated pipeline was developed for the identification of B-Cell, MHC (Major histocompatibility complex) class I and II epitopes. KEY FINDINGS Phase I identified the shreds of evidence of reductive evolution and propensity of the Pan-genome of Mycobacteroides getting closed soon. Phase II and Phase III produced 8 vaccine constructs. Our final vaccine construct, V6 qualified for all tests such as absence for allergenicity, presence of antigenicity, etc. V6 contains β-defensin as an adjuvant, linkers, Lysosomal-associated membrane protein 1 (LAMP1) signal peptide, and PADRE (Pan HLA-DR epitopes) amino acid sequence. Besides, V6 also interacts with a maximum number of MHC molecules and the TLR4/MD2 (Toll-like receptor 4/Myeloid differentiation factor 2) complex confirmed by docking and molecular dynamics simulation studies. SIGNIFICANCE The knowledge harnessed from the current study can help improve the current treatment regimens or in an event of an outbreak and propel further related studies.
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Affiliation(s)
- Rohit Satyam
- Department of Biotechnology, Noida Institute of Engineering and Technology (NIET), Greater Noida, India
| | - Tulika Bhardwaj
- Institute of Clinical Medicine, University of Eastern Finland, Kuopio Campus, Finland
| | - Niraj Kumar Jha
- Department of Biotechnology, School of Engineering & Technology (SET), Sharda University, Greater Noida, India.
| | - Saurabh Kumar Jha
- Department of Biotechnology, School of Engineering & Technology (SET), Sharda University, Greater Noida, India
| | - Parma Nand
- Department of Biotechnology, School of Engineering & Technology (SET), Sharda University, Greater Noida, India
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131
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Sunita, Sajid A, Singh Y, Shukla P. Computational tools for modern vaccine development. Hum Vaccin Immunother 2020; 16:723-735. [PMID: 31545127 PMCID: PMC7227725 DOI: 10.1080/21645515.2019.1670035] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 08/28/2019] [Accepted: 09/13/2019] [Indexed: 12/12/2022] Open
Abstract
Vaccines play an essential role in controlling the rates of fatality and morbidity. Vaccines not only arrest the beginning of different diseases but also assign a gateway for its elimination and reduce toxicity. This review gives an overview of the possible uses of computational tools for vaccine design. Moreover, we have described the initiatives of utilizing the diverse computational resources by exploring the immunological databases for developing epitope-based vaccines, peptide-based drugs, and other resources of immunotherapeutics. Finally, the applications of multi-graft and multivalent scaffolding, codon optimization and antibodyomics tools in identifying and designing in silico vaccine candidates are described.
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Affiliation(s)
- Sunita
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
- Bacterial Pathogenesis Laboratory, Department of Zoology, University of Delhi, Delhi
| | - Andaleeb Sajid
- National Institutes of Health, National Cancer Institute, Bethesda, MD, USA
| | - Yogendra Singh
- Bacterial Pathogenesis Laboratory, Department of Zoology, University of Delhi, Delhi
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
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132
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J B, Numbi Ramudu K, Mm B. An efficient single pot DNA recombination method for protein library generation. Int J Biol Macromol 2020; 146:661-667. [PMID: 31874268 DOI: 10.1016/j.ijbiomac.2019.12.191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 12/20/2019] [Accepted: 12/20/2019] [Indexed: 11/28/2022]
Abstract
A simple single pot method was developed to generate a library of protein hybrids/chimeras from unrelated parents. This method allows unbiased facile DNA shuffling based recombination between the parents with the introduction of type IIB restriction enzyme, BsaXI, at multiple distinct crossover sites. To assess this methodology, B1 immunoglobulin domain of protein G and top7 were recombined at four sites, yielding 25 (32) possible hybrid proteins. Tandem colony multiplex PCR based screening was followed to screen the hybrid clones and, sequencing analysis confirmed seven hybrid clones with no sequence bias.
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Affiliation(s)
- Brindha J
- Chemistry Division, School of Advanced Sciences, Vellore Institute of Technology, Chennai campus, Vandalur-Kelambakkam Road, Chennai 600 127, Tamil Nadu, India
| | - Kamini Numbi Ramudu
- Department of Biotechnology, Central Leather Research Institute, Adyar, Chennai 600 020, India
| | - Balamurali Mm
- Chemistry Division, School of Advanced Sciences, Vellore Institute of Technology, Chennai campus, Vandalur-Kelambakkam Road, Chennai 600 127, Tamil Nadu, India.
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133
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Stepwise optimization of recombinant protein production in Escherichia coli utilizing computational and experimental approaches. Appl Microbiol Biotechnol 2020; 104:3253-3266. [DOI: 10.1007/s00253-020-10454-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 01/28/2020] [Accepted: 02/07/2020] [Indexed: 12/14/2022]
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134
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Laurenceau R, Bliem C, Osburne MS, Becker JW, Biller SJ, Cubillos-Ruiz A, Chisholm SW. Toward a genetic system in the marine cyanobacterium Prochlorococcus. Access Microbiol 2020; 2:acmi000107. [PMID: 33005871 PMCID: PMC7523629 DOI: 10.1099/acmi.0.000107] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 01/30/2020] [Indexed: 11/26/2022] Open
Abstract
As the smallest and most abundant primary producer in the oceans, the cyanobacterium Prochlorococcus is of interest to diverse branches of science. For the past 30 years, research on this minimal phototroph has led to a growing understanding of biological organization across multiple scales, from the genome to the global ocean ecosystem. Progress in understanding drivers of its diversity and ecology, as well as molecular mechanisms underpinning its streamlined simplicity, has been hampered by the inability to manipulate these cells genetically. Multiple attempts have been made to develop an efficient genetic transformation method for Prochlorococcus over the years; all have been unsuccessful to date, despite some success with their close relative, Synechococcus. To avoid the pursuit of unproductive paths, we report here what has not worked in our hands, as well as our progress developing a method to screen the most efficient electroporation parameters for optimal DNA delivery into Prochlorococcus cells. We also report a novel protocol for obtaining axenic colonies and a new method for differentiating live and dead cells. The electroporation method can be used to optimize DNA delivery into any bacterium, making it a useful tool for advancing transformation systems in other genetically recalcitrant microorganisms.
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Affiliation(s)
- Raphaël Laurenceau
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Christina Bliem
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Marcia S Osburne
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Present address: Department of Molecular Biology and Microbiology Tufts University School of Medicine, Boston, MA, USA
| | - Jamie W Becker
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Present address: Department of Biology, Haverford College, Haverford, PA, USA
| | - Steven J Biller
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Present address: Department of Biological Sciences, Wellesley College, Wellesley, MA, USA
| | - Andres Cubillos-Ruiz
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Present address: Institute for Medical Engineering and Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA.,Present address: Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Present address: Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Sallie W Chisholm
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
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135
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Ren H, Shi C, Zhao H. Computational Tools for Discovering and Engineering Natural Product Biosynthetic Pathways. iScience 2020; 23:100795. [PMID: 31926431 PMCID: PMC6957853 DOI: 10.1016/j.isci.2019.100795] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 11/24/2019] [Accepted: 12/19/2019] [Indexed: 01/09/2023] Open
Abstract
Natural products (NPs), also known as secondary metabolites, are produced in bacteria, fungi, and plants. NPs represent a rich source of antibacterial, antifungal, and anticancer agents. Recent advances in DNA sequencing technologies and bioinformatics unveiled nature's great potential for synthesizing numerous NPs that may confer unprecedented structural and biological features. However, discovering novel bioactive NPs by genome mining remains a challenge. Moreover, even with interesting bioactivity, the low productivity of many NPs significantly limits their practical applications. Here we discuss the progress in developing bioinformatics tools for efficient discovery of bioactive NPs. In addition, we highlight computational methods for optimizing the productivity of NPs of pharmaceutical importance.
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Affiliation(s)
- Hengqian Ren
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Chengyou Shi
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Departments of Chemistry, Biochemistry, and Bioengineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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136
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Neves D, Vos S, Blank LM, Ebert BE. Pseudomonas mRNA 2.0: Boosting Gene Expression Through Enhanced mRNA Stability and Translational Efficiency. Front Bioeng Biotechnol 2020; 7:458. [PMID: 32039175 PMCID: PMC6993053 DOI: 10.3389/fbioe.2019.00458] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 12/19/2019] [Indexed: 11/14/2022] Open
Abstract
High gene expression of enzymes partaking in recombinant production pathways is a desirable trait among cell factories belonging to all different kingdoms of life. High enzyme abundance is generally aimed for by utilizing strong promoters, which ramp up gene transcription and mRNA levels. Increased protein abundance can alternatively be achieved by optimizing the expression on the post-transcriptional level. Here, we evaluated protein synthesis with a previously proposed optimized gene expression architecture, in which mRNA stability and translation initiation are modulated by genetic parts such as self-cleaving ribozymes and a bicistronic design, which have initially been described to support the standardization of gene expression. The optimized gene expression architecture was tested in Pseudomonas taiwanensis VLB120, a promising, novel microbial cell factory. The expression cassette was employed on a plasmid basis and after single genomic integration. We used three constitutive and two inducible promoters to drive the expression of two fluorescent reporter proteins and a short acetoin biosynthesis pathway. The performance was confronted with that of a traditional expression cassette harboring the same promoter and gene of interest but lacking the genetic parts for increased expression efficiency. The optimized expression cassette granted higher protein abundance independently of the expression basis or promoter used proving its value for applications requiring high protein abundance.
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Affiliation(s)
- Dário Neves
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Aachen, Germany
| | - Stefan Vos
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Aachen, Germany
| | - Lars M Blank
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Aachen, Germany
| | - Birgitta E Ebert
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Aachen, Germany.,Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia.,CSIRO Synthetic Biology Future Science Platform, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Brisbane, QLD, Australia
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137
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Bordbar A, Bagheri KP, Ebrahimi S, Parvizi P. Bioinformatics analyses of immunogenic T-cell epitopes of LeIF and PpSP15 proteins from Leishmania major and sand fly saliva used as model antigens for the design of a multi-epitope vaccine to control leishmaniasis. INFECTION GENETICS AND EVOLUTION 2020; 80:104189. [PMID: 31931259 DOI: 10.1016/j.meegid.2020.104189] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 01/05/2020] [Accepted: 01/08/2020] [Indexed: 11/17/2022]
Abstract
Leishmaniasis is caused by protozoan parasites belonging to 20 Leishmania species. This infectious disease is transmitted by bites of infected phlebotomine sandflies, and is widespread in 97 countries throughout the world. No preventive or effective vaccine has been developed yet. In this study, diverse computational methods were integrated to calculate evolutionary divergence, immunogenicity, IFN-γ production, epitope conservancy, and population coverage of protein fusion models of LeIF-SP15 namely SaLeish. Immunogenicity of LeIF of Leishmania species and SP15 of sandfly saliva has not been investigated in-silico in fusion form. A complete set of 9-mer MHC class I and 15-mer MHC class II peptides were identified with a high affinity for the antigenic epitopes of SaLeish inducing specific responses of CD8+ and CD4+ T cells from BALB/c and human. Our preferred approach was determining truncated fragment of SaLeish rather than a whole length bearing the capacity to trigger specific immune response. Phylogenetic analysis showed that LeIF protein is under balancing selection and is conserved between different Leishmania species. Selected SaLeish model contained 19 and 35 antigenic peptides for MHC class I and II, respectively, with strong binding affinity to both highly frequent HLA-I and HLA-II alleles. Analysis of class I CTL epitopes showed that promiscuous peptides of KSLKADIRK, MSCIPHCKY, LQAGVIVAV, and YQYYGFVAM have greater affinity to interact with HLA-A*01:01, HLA-A*02 (03, 06), HLA-A*30:02, HLA-B*40:01, and HLA-B*52:01 molecules. Population coverage with a range of 78-85% confirmed SaLeish-Model4 as an appropriate vaccine candidate among Persian, South Asia, Europe, and North America population. Also, predicted antigenic epitopes of AKPEIRTFSNVLIKY, TRVQDDLRKLQAGVI, and VALFSATMPEEVLEL corresponding to MHC class II were found to provide strong ability to produce IFNγ toward TH(1)-biased-DTH responses. Findings of the current investigation warrant the future experimental assessment of promising SaLeish prophylaxis vaccine that is capable to enhance both innate and specific cellular immune responses.
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Affiliation(s)
- Ali Bordbar
- Molecular Systematics Laboratory, Parasitology Department, Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran.
| | - Kamran Pooshang Bagheri
- Venom and Biotherapeutics Molecules Lab., Biotechnology Dept., Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Sahar Ebrahimi
- Molecular Systematics Laboratory, Parasitology Department, Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Parviz Parvizi
- Molecular Systematics Laboratory, Parasitology Department, Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran.
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138
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Sinitski D, Gruner K, Bernhagen J, Panstruga R. Studying Plant MIF/D-DT-Like Genes and Proteins (MDLs). Methods Mol Biol 2020; 2080:249-261. [PMID: 31745887 DOI: 10.1007/978-1-4939-9936-1_22] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Human macrophage migration inhibitory factor (MIF) is an inflammatory cytokine with chemokine-like characteristics and an upstream regulator of host innate immunity. It is a critical mediator of a variety of human diseases, such as acute and chronic inflammatory diseases, autoimmunity, atherosclerosis, and cancer. MIF is an atypical chemokine that not only signals through its cognate receptor CD74, but also interacts with the classical chemokine receptors CXCR2 and CXCR4. MIF and its homolog D-dopachrome tautomerase (D-DT)/MIF-2 are structurally unique proteins that are conserved across kingdoms and that share a remarkable homology with bacterial tautomerases/isomerases, albeit the relevance of the tautomerase activity in mammalian systems has remained unclear. Intriguingly, in silico analysis also predicts MIF orthologs in plants such as in the model plant Arabidopsis thaliana. There are three predicted MIF orthologs in A. thaliana, which have been termed A. thaliana MIF/D-DT-like proteins (AtMDLs). Anticipating that there will be a future research interest in studying AtMDLs or other plant MDLs, here we describe methods how to clone, recombinantly express and purify AtMDL proteins, taking into account codon usage differences between plant and mammalian cell systems.
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Affiliation(s)
- Dzmitry Sinitski
- Vascular Biology, Institute for Stroke and Dementia Research, Klinikum der Universitaet Muenchen, Ludwig-Maximilians-University (LMU) Munich, Munich, Germany
| | - Katrin Gruner
- Institute for Biology I, Unit of Plant Molecular Cell Biology, RWTH Aachen University, Aachen, Germany
| | - Jürgen Bernhagen
- Vascular Biology, Institute for Stroke and Dementia Research (ISD), Klinikum der Universitaet Muenchen, Ludwig-Maximilians-University (LMU) Munich, Munich, Germany.
- Munich Heart Alliance, Munich, Germany.
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.
| | - Ralph Panstruga
- Institute for Biology I, Unit of Plant Molecular Cell Biology, RWTH Aachen University, Aachen, Germany.
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139
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Poliner E, Clark E, Cummings C, Benning C, Farre EM. A high-capacity gene stacking toolkit for the oleaginous microalga, Nannochloropsis oceanica CCMP1779. ALGAL RES 2020. [DOI: 10.1016/j.algal.2019.101664] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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140
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González-Benjumea A, Carro J, Renau-Mínguez C, Linde D, Fernández-Fueyo E, Gutiérrez A, Martínez AT. Fatty acid epoxidation byCollariella virescensperoxygenase and heme-channel variants. Catal Sci Technol 2020. [DOI: 10.1039/c9cy02332a] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new unspecific peroxygenase (UPO) generating a variety of epoxidized derivatives of unsaturated fatty acids has been discovered and engineered by heterologous expression of a putativeupogene.
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Affiliation(s)
| | - Juan Carro
- Centro de Investigaciones Biológicas
- CSIC
- E-28040 Madrid
- Spain
| | | | - Dolores Linde
- Centro de Investigaciones Biológicas
- CSIC
- E-28040 Madrid
- Spain
| | | | - Ana Gutiérrez
- Instituto de Recursos Naturales y Agrobiología de Sevilla
- CSIC
- E-41012 Sevilla
- Spain
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141
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Vartiainen E, Blomberg P, Ilmén M, Andberg M, Toivari M, Penttilä M. Evaluation of synthetic formaldehyde and methanol assimilation pathways in Yarrowia lipolytica. Fungal Biol Biotechnol 2019; 6:27. [PMID: 31890234 PMCID: PMC6918578 DOI: 10.1186/s40694-019-0090-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 12/03/2019] [Indexed: 11/10/2022] Open
Abstract
Background Crude glycerol coming from biodiesel production is an attractive carbon source for biological production of chemicals. The major impurity in preparations of crude glycerol is methanol, which is toxic for most microbes. Development of microbes, which would not only tolerate the methanol, but also use it as co-substrate, would increase the feasibility of bioprocesses using crude glycerol as substrate. Results To prevent methanol conversion to CO2 via formaldehyde and formate, the formaldehyde dehydrogenase (FLD) gene was identified in and deleted from Yarrowia lipolytica. The deletion strain was able to convert methanol to formaldehyde without expression of heterologous methanol dehydrogenases. Further, it was shown that expression of heterologous formaldehyde assimilating enzymes could complement the deletion of FLD. The expression of either 3-hexulose-6-phosphate synthase (HPS) enzyme of ribulose monosphosphate pathway or dihydroxyacetone synthase (DHAS) enzyme of xylulose monosphosphate pathway restored the formaldehyde tolerance of the formaldehyde sensitive Δfld1 strain. Conclusions In silico, the expression of heterologous formaldehyde assimilation pathways enable Y. lipolytica to use methanol as substrate for growth and metabolite production. In vivo, methanol was shown to be converted to formaldehyde and the enzymes of formaldehyde assimilation were actively expressed in this yeast. However, further development is required to enable Y. lipolytica to efficiently use methanol as co-substrate with glycerol.
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Affiliation(s)
- Eija Vartiainen
- VTT Technical Research Centre of Finland Ltd, P.O. Box 1000, 02044 VTT Espoo, Finland
| | - Peter Blomberg
- VTT Technical Research Centre of Finland Ltd, P.O. Box 1000, 02044 VTT Espoo, Finland
| | - Marja Ilmén
- VTT Technical Research Centre of Finland Ltd, P.O. Box 1000, 02044 VTT Espoo, Finland
| | - Martina Andberg
- VTT Technical Research Centre of Finland Ltd, P.O. Box 1000, 02044 VTT Espoo, Finland
| | - Mervi Toivari
- VTT Technical Research Centre of Finland Ltd, P.O. Box 1000, 02044 VTT Espoo, Finland
| | - Merja Penttilä
- VTT Technical Research Centre of Finland Ltd, P.O. Box 1000, 02044 VTT Espoo, Finland
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142
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HIV-1 Reverse Transcriptase Promotes Tumor Growth and Metastasis Formation via ROS-Dependent Upregulation of Twist. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2019; 2019:6016278. [PMID: 31885806 PMCID: PMC6915010 DOI: 10.1155/2019/6016278] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 11/01/2019] [Accepted: 11/05/2019] [Indexed: 12/15/2022]
Abstract
HIV-induced immune suppression results in the high prevalence of HIV/AIDS-associated malignancies including Kaposi sarcoma, non-Hodgkin lymphoma, and cervical cancer. HIV-infected people are also at an increased risk of “non-AIDS-defining” malignancies not directly linked to immune suppression but associated with viral infections. Their incidence is increasing despite successful antiretroviral therapy. The mechanism behind this phenomenon remains unclear. Here, we obtained daughter clones of murine mammary gland adenocarcinoma 4T1luc2 cells expressing consensus reverse transcriptase of HIV-1 subtype A FSU_A strain (RT_A) with and without primary mutations of drug resistance. In in vitro tests, mutations of resistance to nucleoside inhibitors K65R/M184V reduced the polymerase, and to nonnucleoside inhibitors K103N/G190S, the RNase H activities of RT_A. Expression of these RT_A variants in 4T1luc2 cells led to increased production of the reactive oxygen species (ROS), lipid peroxidation, enhanced cell motility in the wound healing assay, and upregulation of expression of Vimentin and Twist. These properties, particularly, the expression of Twist, correlated with the levels of expression RT_A and/or the production of ROS. When implanted into syngeneic BALB/C mice, 4T1luc2 cells expressing nonmutated RT_A demonstrated enhanced rate of tumor growth and increased metastatic activity, dependent on the level of expression of RT_A and Twist. No enhancement was observed for the clones expressing mutated RT_A variants. Plausible mechanisms are discussed involving differential interactions of mutated and nonmutated RTs with its cellular partners involved in the regulation of ROS. This study establishes links between the expression of HIV-1 RT, production of ROS, induction of EMT, and enhanced propagation of RT-expressing tumor cells. Such scenario can be proposed as one of the mechanisms of HIV-induced/enhanced carcinogenesis not associated with immune suppression.
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143
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Otto M, Wynands B, Lenzen C, Filbig M, Blank LM, Wierckx N. Rational Engineering of Phenylalanine Accumulation in Pseudomonas taiwanensis to Enable High-Yield Production of Trans-Cinnamate. Front Bioeng Biotechnol 2019; 7:312. [PMID: 31824929 PMCID: PMC6882275 DOI: 10.3389/fbioe.2019.00312] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 10/23/2019] [Indexed: 12/31/2022] Open
Abstract
Microbial biocatalysis represents a promising alternative for the production of a variety of aromatic chemicals, where microorganisms are engineered to convert a renewable feedstock under mild production conditions into a valuable chemical building block. This study describes the rational engineering of the solvent-tolerant bacterium Pseudomonas taiwanensis VLB120 toward accumulation of L-phenylalanine and its conversion into the chemical building block t-cinnamate. We recently reported rational engineering of Pseudomonas toward L-tyrosine accumulation by the insertion of genetic modifications that allow both enhanced flux and prevent aromatics degradation. Building on this knowledge, three genes encoding for enzymes involved in the degradation of L-phenylalanine were deleted to allow accumulation of 2.6 mM of L-phenylalanine from 20 mM glucose. The amino acid was subsequently converted into the aromatic model compound t-cinnamate by the expression of a phenylalanine ammonia-lyase (PAL) from Arabidopsis thaliana. The engineered strains produced t-cinnamate with yields of 23 and 39% Cmol Cmol−1 from glucose and glycerol, respectively. Yields were improved up to 48% Cmol Cmol−1 from glycerol when two enzymes involved in the shikimate pathway were additionally overexpressed, however with negative impact on strain performance and reproducibility. Production titers were increased in fed-batch fermentations, in which 33.5 mM t-cinnamate were produced solely from glycerol, in a mineral medium without additional complex supplements. The aspect of product toxicity was targeted by the utilization of a streamlined, genome-reduced strain, which improves upon the already high tolerance of P. taiwanensis VLB120 toward t-cinnamate.
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Affiliation(s)
- Maike Otto
- Institute of Bio- and Geosciences (IBG-1: Biotechnology), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Benedikt Wynands
- Institute of Bio- and Geosciences (IBG-1: Biotechnology), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Christoph Lenzen
- Institute of Applied Microbiology, Rheinisch-Westfälische Technische Hochschule (RWTH) Aachen University, Aachen, Germany
| | - Melanie Filbig
- Institute of Applied Microbiology, Rheinisch-Westfälische Technische Hochschule (RWTH) Aachen University, Aachen, Germany
| | - Lars M Blank
- Institute of Applied Microbiology, Rheinisch-Westfälische Technische Hochschule (RWTH) Aachen University, Aachen, Germany
| | - Nick Wierckx
- Institute of Bio- and Geosciences (IBG-1: Biotechnology), Forschungszentrum Jülich GmbH, Jülich, Germany
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144
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Gonzalez-Garcia RA, McCubbin T, Turner MS, Nielsen LK, Marcellin E. Engineering Escherichia coli for propionic acid production through the Wood-Werkman cycle. Biotechnol Bioeng 2019; 117:167-183. [PMID: 31556457 DOI: 10.1002/bit.27182] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 09/20/2019] [Accepted: 09/22/2019] [Indexed: 12/15/2022]
Abstract
Native to propionibacteria, the Wood-Werkman cycle enables propionate production via succinate decarboxylation. Current limitations in engineering propionibacteria strains have redirected attention toward the heterologous production in model organisms. Here, we report the functional expression of the Wood-Werkman cycle in Escherichia coli to enable propionate and 1-propanol production. The initial proof-of-concept attempt showed that the cycle can be used for production. However, production levels were low (0.17 mM). In silico optimization of the expression system by operon rearrangement and ribosomal-binding site tuning improved performance by fivefold. Adaptive laboratory evolution further improved performance redirecting almost 30% of total carbon through the Wood-Werkman cycle, achieving propionate and propanol titers of 9 and 5 mM, respectively. Rational engineering to reduce the generation of byproducts showed that lactate (∆ldhA) and formate (∆pflB) knockout strains exhibit an improved propionate and 1-propanol production, while the ethanol (∆adhE) knockout strain only showed improved propionate production.
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Affiliation(s)
- Ricardo A Gonzalez-Garcia
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, Queensland, Australia
| | - Timothy McCubbin
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, Queensland, Australia
| | - Mark S Turner
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, Queensland, Australia.,Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Queensland, Australia
| | - Lars K Nielsen
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, Queensland, Australia
| | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, Queensland, Australia
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145
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Varnosfaderani ZG, Emamzadeh R, Nazari M, Zarean M. Detection of a prostate cancer cell line using a bioluminescent affiprobe: An attempt to develop a new molecular probe for ex vivo studies. Int J Biol Macromol 2019; 138:755-763. [DOI: 10.1016/j.ijbiomac.2019.07.085] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 06/26/2019] [Accepted: 07/11/2019] [Indexed: 11/16/2022]
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146
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Gonzalez-Sanchez B, Vega-Rodríguez MA, Santander-Jiménez S. Multi-objective protein encoding: Redefinition of the problem, new problem-aware operators, and approach based on Variable Neighborhood Search. Inf Sci (N Y) 2019. [DOI: 10.1016/j.ins.2019.05.088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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147
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Mohseni Moghadam Z, Halabian R, Sedighian H, Behzadi E, Amani J, Imani Fooladi AA. Designing and Analyzing the Structure of DT-STXB Fusion Protein as an Anti-tumor Agent: An in Silico Approach. IRANIAN JOURNAL OF PATHOLOGY 2019; 14:305-312. [PMID: 31754360 PMCID: PMC6824772 DOI: 10.30699/ijp.2019.101200.2004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Accepted: 08/22/2019] [Indexed: 01/24/2023]
Abstract
BACKGROUND & OBJECTIVE A main contest in chemotherapy is to obtain regulator above the biodistribution of cytotoxic drugs. The utmost promising strategy comprises of drugs coupled with a tumor-targeting bearer that results in wide cytotoxic activity and particular delivery. The B-subunit of Shiga toxin (STxB) is nontoxic and possesses low immunogenicity that exactly binds to the globotriaosylceramide (Gb3/CD77). Gb3/CD77 extremely expresses on a number of human tumors such as pancreatic, colon, and breast cancer and acts as a functional receptor for Shiga toxin (STx). Then, this toxin can be applied to target Gb3-positive human tumors. In this study, we evaluated DT390-STXB chimeric protein as a new anti-tumor candidate via genetically fusing the DT390 fragment of DT538 (Native diphtheria toxin) to STxB. METHODS This study intended to investigate the DT390- STxB fusion protein structure in silico. Considering the Escherichia coli codon usage, the genomic construct was designed. The properties and the structure of the protein were determined by an in silico technique. The mRNA structure and the physicochemical characteristics, construction, and the stability of the designed chimeric protein were analyzed using computational and bioinformatics tools and servers. Hence, the GOR4 and I-TASSER online web servers were used to predict the secondary and tertiary structures of the designed protein. RESULTS The results demonstrated that codon adaptation index (CAI) of dt390-stxB chimeric gene raised from 0.6 in the wild type to 0.9 in the chimeric optimized gene. The mfold data revealed that the dt390-stxB mRNA was completely stable to be translated effectively in the novel host. The normal activity of the fusion protein determined by considering the secondary and tertiary structure of each construct. Energy calculation data indicated that the thermodynamic ensemble for mRNA structure was -427.40 kJ/mol. The stability index (SI) of DT390-STxB was 36.95, which is quite appropriate to preserve the stability of the construct. Ultimately, the DT390-STxB was classified as a steady fusion protein according to the Ramachandran plot. CONCLUSION Our results showed that DT390-STXB was a stable chimeric protein and it can be recruited as a candidate of novel anti-tumor agents for the development of breast cancer treatment.
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Affiliation(s)
- Zeynab Mohseni Moghadam
- Applied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Raheleh Halabian
- Applied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Hamid Sedighian
- Applied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Elham Behzadi
- Department of Microbiology, College of Basic Sciences, Shahr-e-Qods Branch, Islamic Azad University, Tehran, Iran
| | - Jafar Amani
- Applied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Abbas Ali Imani Fooladi
- Applied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
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148
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Bahrami AA, Payandeh Z, Khalili S, Zakeri A, Bandehpour M. Immunoinformatics: In Silico Approaches and Computational Design of a Multi-epitope, Immunogenic Protein. Int Rev Immunol 2019; 38:307-322. [PMID: 31478759 DOI: 10.1080/08830185.2019.1657426] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Immunoinformatics is a new critical field with several tools and databases that conduct the eyesight of experimental selection and facilitate analysis of the great amount of immunologic data obtained from experimental researches and helps to design and introducing new hypothesis. Given these visages, immunoinformatics seems to be the way that develop and progress the immunological research. Bioinformatics methods and applications are successfully employed in vaccine informatics to assist different sites of the preclinical, clinical, and post-licensure vaccine enterprises. On the other hand, the progression of molecular biology and immunology caused epitope vaccines have become the focus of research on molecular vaccines. Moreover, reverse vaccinology could improve vaccine production and vaccination protocols by in silico prediction of protein-vaccine candidates from genome sequences. B- and T-cell immune epitopes could be predicted by immunoinformatics algorithms and computational methods to improve the vaccine design, protective immunity analysis, assessment of vaccine safety and efficacy, and immunization modeling. This review aims to discuss the power of computational approaches in vaccine design and their relevance to the development of effective vaccines. Furthermore, the various divisions of this field and available tools in each item are introduced and reviewed.
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Affiliation(s)
- Armina Alagheband Bahrami
- Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zahra Payandeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Saeed Khalili
- Department of Biology Sciences, Shahid Rajaee Teacher Training University, Tehran, Iran
| | - Alireza Zakeri
- Department of Biology Sciences, Shahid Rajaee Teacher Training University, Tehran, Iran
| | - Mojgan Bandehpour
- Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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149
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In-silico design and production of a novel antigenic chimeric Shigella IpaB fused to C-terminal of Clostridium perfringens enterotoxin. Mol Biol Rep 2019; 46:6105-6115. [PMID: 31473892 DOI: 10.1007/s11033-019-05046-5] [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: 03/22/2019] [Accepted: 08/27/2019] [Indexed: 10/26/2022]
Abstract
The emergence of antibiotic-resistant phenotypes in Shigella serotypes and the high mortality rate, approximately one million dead annually, in affected patients announce a global demand for an effective serotype-independent vaccine against Shigella. This study aims to design, express, and purify a novel chimeric protein, as a serotype-independent vaccine candidate against Shigella containing full-length Shigella invasion plasmid antigen B (IpaB) and a C-terminal fragment (residues 194-319) of Clostridium perfringens enterotoxin (C-CPE) as a mucosal adjuvant. Several online databases and bioinformatics software were utilized to design the chimeric protein and the relative recombinant gene. The recombinant gene encoding IpaB-CPE194-319 was synthesized, cloned into pACYCDuet-1 expression vector, and transferred to E. coli Bl21 (DE3) cells. IpaB-CPE194-319 was then expressed in auto-induction medium, purified and characterized using MALDI-TOF-TOF mass spectrometry. Followed by subcutaneous injection of the purified IpaB-CPE194-319 to BALB/c mice, antigenicity of this chimeric protein was determined through performing dot-blot immunoassay on nitrocellulose membrane using mice sera. The outcomes of this study show the successful design, efficient expression, and purification of IpaB-CPE194-319 divalent chimeric protein under mentioned conditions. The obtained results also demonstrate the intrinsic antigenic property of IpaB-CPE194-319.
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150
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Taylor GM, Mordaka PM, Heap JT. Start-Stop Assembly: a functionally scarless DNA assembly system optimized for metabolic engineering. Nucleic Acids Res 2019; 47:e17. [PMID: 30462270 PMCID: PMC6379671 DOI: 10.1093/nar/gky1182] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 11/02/2018] [Accepted: 11/07/2018] [Indexed: 12/20/2022] Open
Abstract
DNA assembly allows individual DNA constructs or libraries to be assembled quickly and reliably. Most methods are either: (i) Modular, easily scalable and suitable for combinatorial assembly, but leave undesirable 'scar' sequences; or (ii) bespoke (non-modular), scarless but less suitable for construction of combinatorial libraries. Both have limitations for metabolic engineering. To overcome this trade-off we devised Start-Stop Assembly, a multi-part, modular DNA assembly method which is both functionally scarless and suitable for combinatorial assembly. Crucially, 3 bp overhangs corresponding to start and stop codons are used to assemble coding sequences into expression units, avoiding scars at sensitive coding sequence boundaries. Building on this concept, a complete DNA assembly framework was designed and implemented, allowing assembly of up to 15 genes from up to 60 parts (or mixtures); monocistronic, operon-based or hybrid configurations; and a new streamlined assembly hierarchy minimizing the number of vectors. Only one destination vector is required per organism, reflecting our optimization of the system for metabolic engineering in diverse organisms. Metabolic engineering using Start-Stop Assembly was demonstrated by combinatorial assembly of carotenoid pathways in Escherichia coli resulting in a wide range of carotenoid production and colony size phenotypes indicating the intended exploration of design space.
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Affiliation(s)
- George M Taylor
- Imperial College Centre for Synthetic Biology, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Paweł M Mordaka
- Imperial College Centre for Synthetic Biology, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - John T Heap
- Imperial College Centre for Synthetic Biology, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
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